diff --git a/Cargo.lock b/Cargo.lock
index aebdbf3b..cda13440 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -259,6 +259,7 @@ dependencies = [
  "shlex",
  "sysinfo",
  "tempfile",
+ "thiserror 2.0.18",
  "time",
  "tiny-bip39",
  "tokio",
diff --git a/crates/atuin-ai/src/commands.rs b/crates/atuin-ai/src/commands.rs
index cdbc8f2d..c6790f55 100644
--- a/crates/atuin-ai/src/commands.rs
+++ b/crates/atuin-ai/src/commands.rs
@@ -1,13 +1,8 @@
-use std::{
-    fs,
-    path::{Path, PathBuf},
-};
-
+use atuin_client::logs::FromSettings;
+use atuin_client::settings::Settings;
+use atuin_common::logs::{FileConfig, LogConfig, StderrConfig};
 use atuin_common::shell::Shell;
 use clap::{Args, Subcommand};
-use eyre::Result;
-use tracing_appender::rolling::{RollingFileAppender, Rotation};
-use tracing_subscriber::{EnvFilter, Layer, fmt, layer::SubscriberExt, util::SubscriberInitExt};
 pub mod init;
 pub(crate) mod inline;
 
@@ -27,7 +22,7 @@ pub struct AiArgs {
 }
 
 #[derive(Subcommand, Debug)]
-pub enum Commands {
+pub enum Command {
     /// Initialize shell integration
     Init {
         /// Shell to generate integration for; defaults to "auto"
@@ -50,109 +45,30 @@ pub enum Commands {
     },
 }
 
-pub async fn run(
-    command: Commands,
-    settings: &atuin_client::settings::Settings,
-) -> eyre::Result<()> {
+impl Command {
+    pub fn log_config(&self, settings: &Settings) -> LogConfig {
+        match self {
+            Self::Inline { args, .. } => LogConfig {
+                file: FileConfig::from_settings(&settings.logs, &settings.logs.ai),
+                stderr: args.verbose.then(StderrConfig::default),
+            },
+            _ => LogConfig::stderr_only(),
+        }
+    }
+}
+
+pub async fn run(command: Command, settings: &Settings) -> eyre::Result<()> {
     match command {
-        Commands::Init { shell } => init::run(shell).await,
-        Commands::Inline {
+        Command::Init { shell } => init::run(shell).await,
+        Command::Inline {
             command,
             hook,
             args,
             ..
-        } => {
-            if settings.logs.ai_enabled() {
-                init_logging(settings, args.verbose)?;
-            }
-
-            inline::run(command, args.api_endpoint, args.api_token, settings, hook).await
-        }
+        } => inline::run(command, args.api_endpoint, args.api_token, settings, hook).await,
     }
 }
 
 pub(crate) fn detect_shell() -> Option<String> {
     Some(Shell::current().to_string())
 }
-
-/// Initializes logging for the AI commands.
-fn init_logging(settings: &atuin_client::settings::Settings, verbose: bool) -> Result<()> {
-    // ATUIN_LOG env var overrides config file level settings
-    let env_log_set = std::env::var("ATUIN_LOG").is_ok();
-
-    // Base filter from env var (or empty if not set)
-    let base_filter =
-        EnvFilter::from_env("ATUIN_LOG").add_directive("sqlx_sqlite::regexp=off".parse()?);
-
-    // Use config level unless ATUIN_LOG is set
-    let filter = if env_log_set {
-        base_filter
-    } else {
-        EnvFilter::default()
-            .add_directive(settings.logs.ai_level().as_directive().parse()?)
-            .add_directive("sqlx_sqlite::regexp=off".parse()?)
-    };
-
-    let log_dir = PathBuf::from(&settings.logs.dir);
-    let ai_log_filename = settings.logs.ai.file.clone();
-
-    // Clean up old log files
-    cleanup_old_logs(&log_dir, &ai_log_filename, settings.logs.ai_retention());
-
-    let console_layer = if verbose {
-        Some(
-            fmt::layer()
-                .with_writer(std::io::stderr)
-                .with_ansi(true)
-                .with_target(false)
-                .with_filter(filter.clone()),
-        )
-    } else {
-        None
-    };
-
-    let file_appender = RollingFileAppender::new(Rotation::DAILY, &log_dir, &ai_log_filename);
-
-    let base = tracing_subscriber::registry().with(
-        fmt::layer()
-            .with_writer(file_appender)
-            .with_ansi(false)
-            .with_filter(filter),
-    );
-
-    if let Some(console_layer) = console_layer {
-        base.with(console_layer).init();
-    } else {
-        base.init();
-    };
-
-    Ok(())
-}
-
-fn cleanup_old_logs(log_dir: &Path, prefix: &str, retention_days: u64) {
-    let cutoff = std::time::SystemTime::now()
-        - std::time::Duration::from_secs(retention_days * 24 * 60 * 60);
-
-    let Ok(entries) = fs::read_dir(log_dir) else {
-        return;
-    };
-
-    for entry in entries.flatten() {
-        let path = entry.path();
-        let Some(name) = path.file_name().and_then(|n| n.to_str()) else {
-            continue;
-        };
-
-        // Match files like "search.log.2024-02-23" or "daemon.log.2024-02-23"
-        if !name.starts_with(prefix) || name == prefix {
-            continue;
-        }
-
-        if let Ok(metadata) = entry.metadata()
-            && let Ok(modified) = metadata.modified()
-            && modified < cutoff
-        {
-            let _ = fs::remove_file(&path);
-        }
-    }
-}
diff --git a/crates/atuin-client/Cargo.toml b/crates/atuin-client/Cargo.toml
index 2ce4949d..3a58b1c0 100644
--- a/crates/atuin-client/Cargo.toml
+++ b/crates/atuin-client/Cargo.toml
@@ -21,9 +21,7 @@ daemon = []
 check-update = []
 
 [dependencies]
-atuin-common = { path = "../atuin-common", version = "18.17.1" }
 derive_more = { workspace = true }
-
 tracing = { workspace = true }
 base64 = { workspace = true }
 time = { workspace = true, features = ["macros", "formatting", "parsing"] }
@@ -80,6 +78,11 @@ palette = { version = "0.7.5", features = ["serializing"] }
 strum_macros = "0.27"
 strum = { version = "0.27", features = ["strum_macros"] }
 
+[dependencies.atuin-common]
+path = "../atuin-common"
+version = "18.17.1"
+features = ["tracing"]
+
 [dev-dependencies]
 tokio = { version = "1", features = ["full"] }
 pretty_assertions = { workspace = true }
diff --git a/crates/atuin-client/src/lib.rs b/crates/atuin-client/src/lib.rs
index e0430999..41b4ff2a 100644
--- a/crates/atuin-client/src/lib.rs
+++ b/crates/atuin-client/src/lib.rs
@@ -22,6 +22,7 @@ pub mod encryption;
 pub mod history;
 pub mod import;
 pub mod logout;
+pub mod logs;
 pub mod meta;
 pub mod ordering;
 pub mod plugin;
diff --git a/crates/atuin-client/src/logs.rs b/crates/atuin-client/src/logs.rs
new file mode 100644
index 00000000..b7ed8640
--- /dev/null
+++ b/crates/atuin-client/src/logs.rs
@@ -0,0 +1,34 @@
+use crate::settings;
+use atuin_common::logs::{FileConfig, LogConfig};
+use std::path::PathBuf;
+
+pub trait FromSettings: Sized {
+    type Output;
+    fn from_settings(settings: &settings::Logs, child: &settings::LogConfig) -> Self::Output;
+}
+
+impl FromSettings for FileConfig {
+    type Output = Option<Self>;
+
+    fn from_settings(settings: &settings::Logs, child: &settings::LogConfig) -> Option<Self> {
+        if !child.enabled.unwrap_or(settings.enabled) {
+            return None;
+        }
+        Some(Self {
+            path: PathBuf::from_iter([&settings.dir, &child.file]),
+            level: child.level.unwrap_or(settings.level),
+            retention_days: child.retention.unwrap_or(settings.retention),
+        })
+    }
+}
+
+impl FromSettings for LogConfig {
+    type Output = Self;
+
+    fn from_settings(settings: &settings::Logs, child: &settings::LogConfig) -> Self {
+        Self {
+            file: FileConfig::from_settings(settings, child),
+            stderr: None,
+        }
+    }
+}
diff --git a/crates/atuin-client/src/settings.rs b/crates/atuin-client/src/settings.rs
index 25a05c6f..c40813c5 100644
--- a/crates/atuin-client/src/settings.rs
+++ b/crates/atuin-client/src/settings.rs
@@ -1,6 +1,4 @@
-use std::{collections::HashMap, io::prelude::*, path::PathBuf, str::FromStr, sync::OnceLock};
-use tokio::sync::OnceCell;
-
+use atuin_common::logs::LogLevel;
 use atuin_common::record::HostId;
 use atuin_common::utils;
 use clap::ValueEnum;
@@ -14,7 +12,9 @@ use regex::RegexSet;
 use semver::Version;
 use serde::{Deserialize, Serialize};
 use serde_with::DeserializeFromStr;
+use std::{collections::HashMap, io::prelude::*, path::PathBuf, str::FromStr, sync::OnceLock};
 use time::{OffsetDateTime, UtcOffset, format_description::FormatItem, macros::format_description};
+use tokio::sync::OnceCell;
 
 pub const HISTORY_PAGE_SIZE: i64 = 100;
 static EXAMPLE_CONFIG: &str = include_str!("../config.toml");
@@ -573,31 +573,6 @@ pub struct Tmux {
     pub height: String,
 }
 
-/// Log level for file logging. Maps to tracing's LevelFilter.
-#[derive(Clone, Copy, Debug, Default, PartialEq, Eq, Deserialize, Serialize)]
-#[serde(rename_all = "lowercase")]
-pub enum LogLevel {
-    Trace,
-    Debug,
-    #[default]
-    Info,
-    Warn,
-    Error,
-}
-
-impl LogLevel {
-    /// Convert to a tracing directive string for use with EnvFilter.
-    pub fn as_directive(&self) -> &'static str {
-        match self {
-            LogLevel::Trace => "trace",
-            LogLevel::Debug => "debug",
-            LogLevel::Info => "info",
-            LogLevel::Warn => "warn",
-            LogLevel::Error => "error",
-        }
-    }
-}
-
 /// Configuration for a specific log type (search or daemon).
 #[derive(Clone, Debug, Default, Deserialize, Serialize)]
 pub struct LogConfig {
@@ -614,6 +589,15 @@ pub struct LogConfig {
     pub retention: Option<u64>,
 }
 
+impl LogConfig {
+    pub fn new(file: impl Into<String>) -> Self {
+        Self {
+            file: file.into(),
+            ..Default::default()
+        }
+    }
+}
+
 #[derive(Clone, Debug, Deserialize, Serialize)]
 pub struct Logs {
     /// Enable file logging globally. Defaults to true.
@@ -632,7 +616,7 @@ pub struct Logs {
     #[serde(default = "Logs::default_retention")]
     pub retention: u64,
 
-    /// Search log settings
+    /// Search log settings; only used with `--interactive`
     #[serde(default)]
     pub search: LogConfig,
 
@@ -763,18 +747,9 @@ impl Default for Logs {
             dir: "".to_string(),
             level: LogLevel::default(),
             retention: Self::default_retention(),
-            search: LogConfig {
-                file: "search.log".to_string(),
-                ..Default::default()
-            },
-            daemon: LogConfig {
-                file: "daemon.log".to_string(),
-                ..Default::default()
-            },
-            ai: LogConfig {
-                file: "ai.log".to_string(),
-                ..Default::default()
-            },
+            search: LogConfig::new("search.log"),
+            daemon: LogConfig::new("daemon.log"),
+            ai: LogConfig::new("ai.log"),
         }
     }
 }
@@ -787,78 +762,6 @@ impl Logs {
     fn default_retention() -> u64 {
         4
     }
-
-    /// Returns whether search logging is enabled.
-    /// Uses search-specific setting if set, otherwise falls back to global.
-    pub fn search_enabled(&self) -> bool {
-        self.search.enabled.unwrap_or(self.enabled)
-    }
-
-    /// Returns whether daemon logging is enabled.
-    /// Uses daemon-specific setting if set, otherwise falls back to global.
-    pub fn daemon_enabled(&self) -> bool {
-        self.daemon.enabled.unwrap_or(self.enabled)
-    }
-
-    /// Returns whether AI logging is enabled.
-    /// Uses AI-specific setting if set, otherwise falls back to global.
-    pub fn ai_enabled(&self) -> bool {
-        self.ai.enabled.unwrap_or(self.enabled)
-    }
-
-    /// Returns the log level for search logging.
-    /// Uses search-specific setting if set, otherwise falls back to global.
-    pub fn search_level(&self) -> LogLevel {
-        self.search.level.unwrap_or(self.level)
-    }
-
-    /// Returns the log level for daemon logging.
-    /// Uses daemon-specific setting if set, otherwise falls back to global.
-    pub fn daemon_level(&self) -> LogLevel {
-        self.daemon.level.unwrap_or(self.level)
-    }
-
-    /// Returns the log level for AI logging.
-    /// Uses AI-specific setting if set, otherwise falls back to global.
-    pub fn ai_level(&self) -> LogLevel {
-        self.ai.level.unwrap_or(self.level)
-    }
-
-    /// Returns the retention days for search logging.
-    /// Uses search-specific setting if set, otherwise falls back to global.
-    pub fn search_retention(&self) -> u64 {
-        self.search.retention.unwrap_or(self.retention)
-    }
-
-    /// Returns the retention days for daemon logging.
-    /// Uses daemon-specific setting if set, otherwise falls back to global.
-    pub fn daemon_retention(&self) -> u64 {
-        self.daemon.retention.unwrap_or(self.retention)
-    }
-
-    /// Returns the retention days for AI logging.
-    /// Uses AI-specific setting if set, otherwise falls back to global.
-    pub fn ai_retention(&self) -> u64 {
-        self.ai.retention.unwrap_or(self.retention)
-    }
-
-    /// Returns the full path for the search log file.
-    pub fn search_path(&self) -> PathBuf {
-        let path = PathBuf::from(&self.search.file);
-        PathBuf::from(&self.dir).join(path)
-    }
-
-    /// Returns the full path for the daemon log file.
-    pub fn daemon_path(&self) -> PathBuf {
-        let path = PathBuf::from(&self.daemon.file);
-        PathBuf::from(&self.dir).join(path)
-    }
-
-    /// Returns the full path for the AI log file.
-    pub fn ai_path(&self) -> PathBuf {
-        let path = PathBuf::from(&self.ai.file);
-        PathBuf::from(&self.dir).join(path)
-    }
 }
 
 impl Default for Search {
diff --git a/crates/atuin-common/Cargo.toml b/crates/atuin-common/Cargo.toml
index 113cd799..02181742 100644
--- a/crates/atuin-common/Cargo.toml
+++ b/crates/atuin-common/Cargo.toml
@@ -14,7 +14,7 @@ repository = { workspace = true }
 
 [features]
 # Enables the `test_utils` module.
-test-utils = ["dep:tracing", "dep:tracing-subscriber"]
+test-utils = ["tracing", "dep:tracing-subscriber"]
 
 [dependencies]
 derive_more = { workspace = true }
diff --git a/crates/atuin-common/src/lib.rs b/crates/atuin-common/src/lib.rs
index 607353d8..cde6302f 100644
--- a/crates/atuin-common/src/lib.rs
+++ b/crates/atuin-common/src/lib.rs
@@ -58,6 +58,7 @@ macro_rules! new_uuid {
 }
 
 pub mod api;
+pub mod logs;
 pub mod record;
 pub mod shell;
 #[cfg(feature = "test-utils")]
diff --git a/crates/atuin-common/src/logs.rs b/crates/atuin-common/src/logs.rs
new file mode 100644
index 00000000..7422511f
--- /dev/null
+++ b/crates/atuin-common/src/logs.rs
@@ -0,0 +1,83 @@
+use serde::{Deserialize, Serialize};
+use std::ffi::OsStr;
+use std::path::{Path, PathBuf};
+
+/// Log level for file logging. Maps to tracing's LevelFilter.
+#[derive(Clone, Copy, Debug, Default, PartialEq, Eq, Deserialize, Serialize)]
+#[serde(rename_all = "lowercase")]
+pub enum LogLevel {
+    Trace,
+    Debug,
+    #[default]
+    Info,
+    Warn,
+    Error,
+}
+
+impl LogLevel {
+    #[cfg(feature = "tracing")]
+    pub fn to_tracing(&self) -> tracing::Level {
+        use tracing::Level;
+        match self {
+            LogLevel::Trace => Level::TRACE,
+            LogLevel::Debug => Level::DEBUG,
+            LogLevel::Info => Level::INFO,
+            LogLevel::Warn => Level::WARN,
+            LogLevel::Error => Level::ERROR,
+        }
+    }
+}
+
+#[derive(Debug)]
+pub struct FileConfig {
+    pub path: PathBuf,
+    pub level: LogLevel,
+    pub retention_days: u64,
+}
+
+impl FileConfig {
+    pub fn directory(&self) -> &Path {
+        self.path.parent().unwrap_or_else(|| Path::new(""))
+    }
+
+    pub fn name(&self) -> &OsStr {
+        self.path.file_name().unwrap_or_else(|| OsStr::new(""))
+    }
+}
+
+#[derive(Debug, Default)]
+pub struct StderrConfig {
+    pub show_time: bool,
+    pub show_target: bool,
+}
+
+impl StderrConfig {
+    pub fn verbose() -> Self {
+        Self {
+            show_time: true,
+            show_target: true,
+        }
+    }
+}
+
+#[derive(Debug)]
+pub struct LogConfig {
+    pub file: Option<FileConfig>,
+    pub stderr: Option<StderrConfig>,
+}
+
+impl LogConfig {
+    pub fn file_only(file: FileConfig) -> Self {
+        Self {
+            file: Some(file),
+            stderr: None,
+        }
+    }
+
+    pub fn stderr_only() -> Self {
+        Self {
+            file: None,
+            stderr: Some(StderrConfig::default()),
+        }
+    }
+}
diff --git a/crates/atuin/Cargo.toml b/crates/atuin/Cargo.toml
index aec120bb..4888a108 100644
--- a/crates/atuin/Cargo.toml
+++ b/crates/atuin/Cargo.toml
@@ -46,7 +46,7 @@ check-update = ["atuin-client/check-update"]
 [dependencies]
 atuin-ai = { path = "../atuin-ai", version = "18.17.1", optional = true, default-features = false }
 atuin-client = { path = "../atuin-client", version = "18.17.1", optional = true, default-features = false }
-atuin-common = { workspace = true }
+atuin-common = { workspace = true, features = ["tracing"] }
 atuin-dotfiles = { workspace = true }
 atuin-history = { workspace = true }
 atuin-daemon = { path = "../atuin-daemon", version = "18.17.1", optional = true, default-features = false }
@@ -91,6 +91,7 @@ norm = { version = "0.1.1", features = ["fzf-v2"] }
 atuin-nucleo-matcher = { workspace = true }
 tempfile = { workspace = true }
 shlex = "1.3.0"
+thiserror = { workspace = true }
 
 # settings editor with comment and relative ordering preservation
 toml_edit = { workspace = true }
diff --git a/crates/atuin/src/command/client.rs b/crates/atuin/src/command/client.rs
index 0048655d..369699a7 100644
--- a/crates/atuin/src/command/client.rs
+++ b/crates/atuin/src/command/client.rs
@@ -1,44 +1,13 @@
-use std::fs::{self, OpenOptions};
-use std::path::{Path, PathBuf};
+use std::path::PathBuf;
 
 use clap::Subcommand;
 use eyre::{Result, WrapErr};
 
+use atuin_client::logs::FromSettings;
 use atuin_client::{
     database::Sqlite, record::sqlite_store::SqliteStore, settings::Settings, theme,
 };
-use tracing_appender::rolling::{RollingFileAppender, Rotation};
-use tracing_subscriber::{
-    Layer, filter::EnvFilter, filter::LevelFilter, fmt, fmt::format::FmtSpan, prelude::*,
-};
-
-fn cleanup_old_logs(log_dir: &Path, prefix: &str, retention_days: u64) {
-    let cutoff = std::time::SystemTime::now()
-        - std::time::Duration::from_secs(retention_days * 24 * 60 * 60);
-
-    let Ok(entries) = fs::read_dir(log_dir) else {
-        return;
-    };
-
-    for entry in entries.flatten() {
-        let path = entry.path();
-        let Some(name) = path.file_name().and_then(|n| n.to_str()) else {
-            continue;
-        };
-
-        // Match files like "search.log.2024-02-23" or "daemon.log.2024-02-23"
-        if !name.starts_with(prefix) || name == prefix {
-            continue;
-        }
-
-        if let Ok(metadata) = entry.metadata()
-            && let Ok(modified) = metadata.modified()
-            && modified < cutoff
-        {
-            let _ = fs::remove_file(&path);
-        }
-    }
-}
+use atuin_common::logs::{self, LogConfig};
 
 #[cfg(feature = "sync")]
 mod sync;
@@ -144,7 +113,7 @@ pub enum Cmd {
     /// Run the AI assistant
     #[cfg(feature = "ai")]
     #[command(subcommand)]
-    Ai(atuin_ai::commands::Commands),
+    Ai(atuin_ai::commands::Command),
 
     /// Start an MCP server exposing history search to AI tools (stdio)
     #[cfg(feature = "ai")]
@@ -179,6 +148,7 @@ impl Cmd {
         // doing anything else. History commands are performance-sensitive and run before and after
         // every shell command, so we want to skip any unnecessary initialization for them.
         let settings = Settings::new().wrap_err("could not load client settings")?;
+        self.init_logging(&settings);
         let theme_manager = theme::ThemeManager::new(settings.theme.debug, None);
         let res = runtime.block_on(self.run_inner(settings, theme_manager));
 
@@ -193,152 +163,6 @@ impl Cmd {
         mut settings: Settings,
         mut theme_manager: theme::ThemeManager,
     ) -> Result<()> {
-        // ATUIN_LOG env var overrides config file level settings
-        let env_log_set = std::env::var("ATUIN_LOG").is_ok();
-
-        // Base filter from env var (or empty if not set)
-        let base_filter =
-            EnvFilter::from_env("ATUIN_LOG").add_directive("sqlx_sqlite::regexp=off".parse()?);
-
-        let is_interactive_search = matches!(&self, Self::Search(cmd) if cmd.is_interactive());
-        // Use file-based logging for interactive search (TUI mode)
-        let use_search_logging = is_interactive_search && settings.logs.search_enabled();
-
-        // Use file-based logging for daemon
-        #[cfg(feature = "daemon")]
-        let use_daemon_logging = matches!(&self, Self::Daemon(_)) && settings.logs.daemon_enabled();
-
-        #[cfg(not(feature = "daemon"))]
-        let use_daemon_logging = false;
-
-        // Check if daemon should also log to console
-        #[cfg(feature = "daemon")]
-        let daemon_show_logs = matches!(&self, Self::Daemon(cmd) if cmd.show_logs());
-
-        #[cfg(not(feature = "daemon"))]
-        let daemon_show_logs = false;
-
-        // Set up span timing JSON logs if ATUIN_SPAN is set
-        let span_path = std::env::var("ATUIN_SPAN").ok().map(|p| {
-            if p.is_empty() {
-                "atuin-spans.json".to_string()
-            } else {
-                p
-            }
-        });
-
-        // Helper to create span timing layer
-        macro_rules! make_span_layer {
-            ($path:expr) => {{
-                let span_file = OpenOptions::new()
-                    .create(true)
-                    .truncate(true)
-                    .write(true)
-                    .open($path)?;
-                Some(
-                    fmt::layer()
-                        .json()
-                        .with_writer(span_file)
-                        .with_span_events(FmtSpan::NEW | FmtSpan::CLOSE)
-                        .with_filter(LevelFilter::TRACE),
-                )
-            }};
-        }
-
-        // Build the subscriber with all configured layers
-        if use_search_logging {
-            let search_filename = settings.logs.search.file.clone();
-            let log_dir = PathBuf::from(&settings.logs.dir);
-            fs::create_dir_all(&log_dir)?;
-
-            // Clean up old log files
-            cleanup_old_logs(&log_dir, &search_filename, settings.logs.search_retention());
-
-            let file_appender =
-                RollingFileAppender::new(Rotation::DAILY, &log_dir, &search_filename);
-
-            // Use config level unless ATUIN_LOG is set
-            let filter = if env_log_set {
-                base_filter
-            } else {
-                EnvFilter::default()
-                    .add_directive(settings.logs.search_level().as_directive().parse()?)
-                    .add_directive("sqlx_sqlite::regexp=off".parse()?)
-            };
-
-            let base = tracing_subscriber::registry().with(
-                fmt::layer()
-                    .with_writer(file_appender)
-                    .with_ansi(false)
-                    .with_filter(filter),
-            );
-
-            match &span_path {
-                Some(sp) => {
-                    base.with(make_span_layer!(sp)).init();
-                }
-                None => {
-                    base.init();
-                }
-            }
-        } else if use_daemon_logging {
-            let daemon_filename = settings.logs.daemon.file.clone();
-            let log_dir = PathBuf::from(&settings.logs.dir);
-            fs::create_dir_all(&log_dir)?;
-
-            // Clean up old log files
-            cleanup_old_logs(&log_dir, &daemon_filename, settings.logs.daemon_retention());
-
-            let file_appender =
-                RollingFileAppender::new(Rotation::DAILY, &log_dir, &daemon_filename);
-
-            // Use config level unless ATUIN_LOG is set
-            let file_filter = if env_log_set {
-                base_filter
-            } else {
-                EnvFilter::default()
-                    .add_directive(settings.logs.daemon_level().as_directive().parse()?)
-                    .add_directive("sqlx_sqlite::regexp=off".parse()?)
-            };
-
-            let file_layer = fmt::layer()
-                .with_writer(file_appender)
-                .with_ansi(false)
-                .with_filter(file_filter);
-
-            // Optionally add console layer for --show-logs
-            if daemon_show_logs {
-                let console_filter = EnvFilter::from_env("ATUIN_LOG")
-                    .add_directive("sqlx_sqlite::regexp=off".parse()?);
-
-                let console_layer = fmt::layer().with_filter(console_filter);
-
-                let base = tracing_subscriber::registry()
-                    .with(file_layer)
-                    .with(console_layer);
-
-                match &span_path {
-                    Some(sp) => {
-                        base.with(make_span_layer!(sp)).init();
-                    }
-                    None => {
-                        base.init();
-                    }
-                }
-            } else {
-                let base = tracing_subscriber::registry().with(file_layer);
-
-                match &span_path {
-                    Some(sp) => {
-                        base.with(make_span_layer!(sp)).init();
-                    }
-                    None => {
-                        base.init();
-                    }
-                }
-            }
-        }
-
         tracing::trace!(command = ?self, "client command");
 
         // Skip initializing any databases for history
@@ -408,4 +232,32 @@ impl Cmd {
             Self::Mcp => atuin_ai::mcp::run(&db).await,
         }
     }
+
+    fn log_config(&self, settings: &Settings) -> Option<LogConfig> {
+        match self {
+            Self::History(cmd) => cmd.log_config(),
+
+            Self::Search(cmd) if cmd.is_interactive() => Some(LogConfig::from_settings(
+                &settings.logs,
+                &settings.logs.search,
+            )),
+
+            #[cfg(feature = "daemon")]
+            Self::Daemon(cmd) => Some(LogConfig {
+                file: logs::FileConfig::from_settings(&settings.logs, &settings.logs.daemon),
+                stderr: cmd.show_logs().then(logs::StderrConfig::verbose),
+            }),
+
+            #[cfg(feature = "ai")]
+            Self::Ai(cmd) => Some(cmd.log_config(settings)),
+
+            _ => Some(LogConfig::stderr_only()),
+        }
+    }
+
+    fn init_logging(&self, settings: &Settings) {
+        if let Some(config) = self.log_config(settings) {
+            crate::logs::init_logging(&config);
+        }
+    }
 }
diff --git a/crates/atuin/src/command/client/history.rs b/crates/atuin/src/command/client/history.rs
index 99ee19f1..ca55f172 100644
--- a/crates/atuin/src/command/client/history.rs
+++ b/crates/atuin/src/command/client/history.rs
@@ -5,6 +5,7 @@ use std::{
     time::Duration,
 };
 
+use atuin_common::logs::LogConfig;
 use atuin_common::utils::{self, Escapable as _};
 use clap::Subcommand;
 use eyre::{Context, Result, bail};
@@ -60,6 +61,11 @@ pub enum Cmd {
         intent: Option<String>,
 
         command: Vec<String>,
+
+        /// Passed by shell hooks; this flag disables logging to avoid corrupting the terminal and
+        /// to minimize the amount of time the command takes to run.
+        #[arg(long, hide = true)]
+        hook: bool,
     },
 
     /// Finishes a new command in the history (adds time, exit code)
@@ -69,6 +75,11 @@ pub enum Cmd {
         exit: i64,
         #[arg(long, short)]
         duration: Option<u64>,
+
+        /// Passed by shell hooks; this flag disables logging to avoid corrupting the terminal and
+        /// to minimize the amount of time the command takes to run.
+        #[arg(long, hide = true)]
+        hook: bool,
     },
 
     /// Stream history events from the daemon as they are received
@@ -1105,6 +1116,7 @@ impl Cmd {
                 author,
                 intent,
                 command,
+                ..
             } => {
                 let command = if cmd_env {
                     std::env::var("ATUIN_COMMAND_LINE").unwrap_or_default()
@@ -1121,9 +1133,9 @@ impl Cmd {
 
                 Ok(())
             }
-            Self::End { id, exit, duration } => {
-                end_history_entry(settings, &id, exit, duration).await
-            }
+            Self::End {
+                id, exit, duration, ..
+            } => end_history_entry(settings, &id, exit, duration).await,
             Self::Tail => {
                 #[cfg(feature = "daemon")]
                 {
@@ -1220,6 +1232,18 @@ impl Cmd {
             }
         }
     }
+
+    fn logs_enabled(&self) -> bool {
+        match self {
+            // Enable logs if not invoked from a shell hook.
+            Self::Start { hook, .. } | Self::End { hook, .. } => !*hook,
+            _ => true,
+        }
+    }
+
+    pub fn log_config(&self) -> Option<LogConfig> {
+        self.logs_enabled().then(LogConfig::stderr_only)
+    }
 }
 
 #[cfg(test)]
diff --git a/crates/atuin/src/command/mod.rs b/crates/atuin/src/command/mod.rs
index 6cd221a4..8ffbab93 100644
--- a/crates/atuin/src/command/mod.rs
+++ b/crates/atuin/src/command/mod.rs
@@ -1,3 +1,4 @@
+use atuin_common::logs::LogConfig;
 use clap::Subcommand;
 use eyre::Result;
 
@@ -48,6 +49,13 @@ impl AtuinCmd {
             umask(mode);
         }
 
+        match self {
+            // Client commands initialize their own logging
+            #[cfg(feature = "client")]
+            Self::Client(_) => {}
+            _ => crate::logs::init_logging(&LogConfig::stderr_only()),
+        }
+
         match self {
             #[cfg(feature = "client")]
             Self::Client(client) => client.run(),
diff --git a/crates/atuin/src/logs.rs b/crates/atuin/src/logs.rs
new file mode 100644
index 00000000..23d75f96
--- /dev/null
+++ b/crates/atuin/src/logs.rs
@@ -0,0 +1,166 @@
+use atuin_common::logs::{FileConfig, LogConfig, StderrConfig};
+use std::fs::OpenOptions;
+use std::io::IsTerminal;
+use tracing::Level;
+use tracing_appender::rolling::{self, RollingFileAppender, Rotation};
+use tracing_subscriber::filter::{self, EnvFilter, LevelFilter};
+use tracing_subscriber::fmt;
+use tracing_subscriber::fmt::format::FmtSpan;
+use tracing_subscriber::prelude::*;
+
+pub fn init_logging(config: &LogConfig) {
+    // We have to dispatch the time config statically; see
+    // https://github.com/tokio-rs/tracing/issues/3180
+    match &config.stderr {
+        Some(StderrConfig {
+            show_time: false, ..
+        }) => with_stderr_time::<()>(config),
+        _ => with_stderr_time::<fmt::time::SystemTime>(config),
+    }
+}
+
+fn get_base_filter(config: &LogConfig) -> EnvFilter {
+    let level = config
+        .file
+        .as_ref()
+        .map_or(Level::WARN, |f| f.level.to_tracing());
+    EnvFilter::default().add_directive(level.into())
+}
+
+fn clean_up_old_logs(config: &FileConfig) {
+    let Some(cutoff) = config
+        .retention_days
+        .checked_mul(24 * 60 * 60)
+        .and_then(|s| std::time::SystemTime::now().checked_sub(std::time::Duration::from_secs(s)))
+    else {
+        return;
+    };
+
+    let Ok(entries) = std::fs::read_dir(config.directory()) else {
+        return;
+    };
+
+    let Some(prefix) = config.name().to_str() else {
+        return;
+    };
+
+    for entry in entries.flatten() {
+        let path = entry.path();
+        let Some(name) = path.file_name().and_then(|n| n.to_str()) else {
+            continue;
+        };
+
+        // Match files like "search.log.2024-02-23" or "daemon.log.2024-02-23"
+        if !name.starts_with(prefix) || name == prefix {
+            continue;
+        }
+
+        if let Ok(metadata) = entry.metadata()
+            && let Ok(modified) = metadata.modified()
+            && modified < cutoff
+        {
+            let _ = std::fs::remove_file(&path);
+        }
+    }
+}
+
+#[derive(Debug, thiserror::Error)]
+enum FileWriterError {
+    #[error("log file name must be utf-8")]
+    NonUtf8Filename,
+    #[error("{0}")]
+    RollingFileAppender(#[from] rolling::InitError),
+}
+
+fn make_file_writer(config: &FileConfig) -> Result<RollingFileAppender, FileWriterError> {
+    let prefix = config
+        .name()
+        .to_str()
+        .ok_or(FileWriterError::NonUtf8Filename)?;
+    let writer = RollingFileAppender::builder()
+        .rotation(Rotation::DAILY)
+        .filename_prefix(prefix)
+        .build(config.directory())?;
+    Ok(writer)
+}
+
+fn with_stderr_time<StderrTime>(config: &LogConfig)
+where
+    StderrTime: fmt::time::FormatTime + Default + Send + Sync + 'static,
+{
+    // ATUIN_LOG env var overrides config file level settings
+    let filter: EnvFilter = std::env::var("ATUIN_LOG")
+        .map_or_else(
+            |_| get_base_filter(config),
+            |s| filter::Builder::default().parse_lossy(s),
+        )
+        .add_directive("sqlx_sqlite::regexp=off".parse().unwrap());
+
+    if let Some(file) = &config.file {
+        clean_up_old_logs(file);
+    }
+
+    let file_layer = config.file.as_ref().map(|file| {
+        let writer = make_file_writer(file)?;
+        let layer = fmt::layer()
+            .with_writer(writer)
+            .with_ansi(false)
+            .with_filter(filter.clone());
+        Ok::<_, FileWriterError>(layer)
+    });
+
+    let stderr_layer = config.stderr.as_ref().map(|stderr| {
+        fmt::layer()
+            .with_writer(std::io::stderr)
+            .with_ansi(std::io::stderr().is_terminal())
+            .with_target(stderr.show_target)
+            .map_event_format(|f| f.with_timer(StderrTime::default()))
+            .with_filter(filter)
+    });
+
+    let span_layer = std::env::var("ATUIN_SPAN").ok().and_then(|value| {
+        let path = if value.is_empty() {
+            "atuin-spans.json".to_owned()
+        } else {
+            value
+        };
+        let file = OpenOptions::new()
+            .create(true)
+            .truncate(true)
+            .write(true)
+            .open(path)
+            .ok()?;
+        let layer = fmt::layer()
+            .json()
+            .with_writer(file)
+            .with_span_events(FmtSpan::NEW | FmtSpan::CLOSE)
+            .with_filter(LevelFilter::TRACE);
+        Some(layer)
+    });
+
+    let (file_layer, file_error) = match file_layer.transpose() {
+        Ok(layer) => (layer, None),
+        Err(e) => (None, Some(e)),
+    };
+    let has_stderr_layer = stderr_layer.is_some();
+
+    if let Err(e) = tracing_subscriber::registry()
+        .with(file_layer)
+        .with(stderr_layer)
+        .with(span_layer)
+        .try_init()
+    {
+        if has_stderr_layer || cfg!(debug_assertions) {
+            eprintln!("failed to initialize logging: {e}");
+        }
+        return;
+    }
+
+    if let Some(e) = file_error {
+        if has_stderr_layer {
+            tracing::warn!("failed to initialize log file: {e}");
+        } else if cfg!(debug_assertions) {
+            eprintln!("failed to initialize log file: {e}");
+        }
+    }
+}
diff --git a/crates/atuin/src/main.rs b/crates/atuin/src/main.rs
index 255db36a..41587abf 100644
--- a/crates/atuin/src/main.rs
+++ b/crates/atuin/src/main.rs
@@ -9,6 +9,7 @@ use eyre::Result;
 use command::AtuinCmd;
 
 mod command;
+pub(crate) mod logs;
 
 #[cfg(feature = "sync")]
 mod print_error;
diff --git a/crates/atuin/src/shell/atuin.bash b/crates/atuin/src/shell/atuin.bash
index 8b540bd7..686439ec 100644
--- a/crates/atuin/src/shell/atuin.bash
+++ b/crates/atuin/src/shell/atuin.bash
@@ -86,7 +86,7 @@ __atuin_preexec() {
     __atuin_update_preexec_backend
 
     local id
-    id=$(atuin history start -- "$1" 2>/dev/null)
+    id=$(atuin history start --hook -- "$1" 2>/dev/null)
     export ATUIN_HISTORY_ID=$id
     [[ -n ${__atuin_skip_osc133:-} ]] || __atuin_osc133_command_executed
     __atuin_preexec_time=${EPOCHREALTIME-}
@@ -141,7 +141,7 @@ __atuin_precmd() {
     fi
 
     [[ -n ${__atuin_skip_osc133:-} ]] || __atuin_osc133_command_finished "$EXIT"
-    (ATUIN_LOG=error atuin history end --exit "$EXIT" ${duration:+"--duration=$duration"} -- "$ATUIN_HISTORY_ID" &) >/dev/null 2>&1
+    (atuin history end --hook --exit "$EXIT" ${duration:+"--duration=$duration"} -- "$ATUIN_HISTORY_ID" >/dev/null 2>&1 &)
     export ATUIN_HISTORY_ID=""
 }
 
@@ -163,7 +163,7 @@ if ((BASH_VERSINFO[0] >= 5 || BASH_VERSINFO[0] == 4 && BASH_VERSINFO[1] >= 4));
     __atuin_evaluate_prompt() {
         __atuin_set_ret_value "${__bp_last_ret_value-}" "${__bp_last_argument_prev_command-}"
         __atuin_prompt=${PS1@P}
-    
+
         # Note: Strip the control characters ^A (\001) and ^B (\002), which
         # Bash internally uses to enclose the escape sequences.  They are
         # produced by '\[' and '\]', respectively, in $PS1 and used to tell
@@ -323,7 +323,7 @@ __atuin_search_cmd() {
         popup_width="${ATUIN_TMUX_POPUP_WIDTH:-80%}" # Keep default value anyways
         popup_height="${ATUIN_TMUX_POPUP_HEIGHT:-60%}"
         tmux display-popup -d "$cdir" -w "$popup_width" -h "$popup_height" -E -E -- \
-            sh -c "PATH='$PATH' ATUIN_SESSION='$ATUIN_SESSION' ATUIN_SHELL=bash ATUIN_LOG=error ATUIN_QUERY='$escaped_query' atuin search $escaped_args -i 2>'$result_file'"
+            sh -c "PATH='$PATH' ATUIN_SESSION='$ATUIN_SESSION' ATUIN_SHELL=bash ATUIN_QUERY='$escaped_query' atuin search $escaped_args -i 2>'$result_file'"
 
         if [[ -f "$result_file" ]]; then
             cat "$result_file"
@@ -332,7 +332,7 @@ __atuin_search_cmd() {
         __atuin_tmux_popup_cleanup
         trap - EXIT HUP INT TERM
     else
-        ATUIN_SHELL=bash ATUIN_LOG=error ATUIN_QUERY=$READLINE_LINE atuin search "${search_args[@]}" -i 3>&1 1>&2 2>&3 3>&-
+        ATUIN_SHELL=bash ATUIN_QUERY=$READLINE_LINE atuin search "${search_args[@]}" -i 3>&1 1>&2 2>&3 3>&-
     fi
 }
 
diff --git a/crates/atuin/src/shell/atuin.fish b/crates/atuin/src/shell/atuin.fish
index 15b33451..96746fe5 100644
--- a/crates/atuin/src/shell/atuin.fish
+++ b/crates/atuin/src/shell/atuin.fish
@@ -20,7 +20,7 @@ end
 
 function _atuin_preexec --on-event fish_preexec
     if not test -n "$fish_private_mode"
-        set -g ATUIN_HISTORY_ID (atuin history start -- "$argv[1]" 2>/dev/null)
+        set -g ATUIN_HISTORY_ID (atuin history start --hook -- "$argv[1]" 2>/dev/null)
         _atuin_osc133_command_executed
     end
 end
@@ -30,7 +30,7 @@ function _atuin_postexec --on-event fish_postexec
 
     if test -n "$ATUIN_HISTORY_ID"
         _atuin_osc133_command_finished $s
-        ATUIN_LOG=error atuin history end --exit $s -- $ATUIN_HISTORY_ID &>/dev/null &
+        atuin history end --hook --exit $s -- $ATUIN_HISTORY_ID &>/dev/null &
         disown
     end
 
@@ -102,7 +102,7 @@ function _atuin_search
         set -l tmpdir (mktemp -d)
         if not test -d "$tmpdir"
             # if mktemp got errors
-            set ATUIN_H (ATUIN_SHELL=fish ATUIN_LOG=error ATUIN_QUERY=(commandline -b) atuin search --keymap-mode=$keymap_mode $argv -i 3>&1 1>&2 2>&3 3>&- | string collect)
+            set ATUIN_H (ATUIN_SHELL=fish ATUIN_QUERY=(commandline -b) atuin search --keymap-mode=$keymap_mode $argv -i 3>&1 1>&2 2>&3 3>&- | string collect)
             set ATUIN_STATUS $pipestatus[1]
         else
             set -l result_file "$tmpdir/result"
@@ -119,7 +119,7 @@ function _atuin_search
             set -l popup_width (test -n "$ATUIN_TMUX_POPUP_WIDTH" && echo "$ATUIN_TMUX_POPUP_WIDTH" || echo "80%")
             set -l popup_height (test -n "$ATUIN_TMUX_POPUP_HEIGHT" && echo "$ATUIN_TMUX_POPUP_HEIGHT" || echo "60%")
             tmux display-popup -d "$cdir" -w "$popup_width" -h "$popup_height" -E -E -- \
-                sh -c "PATH='$PATH' ATUIN_SESSION='$ATUIN_SESSION' ATUIN_SHELL=fish ATUIN_LOG=error ATUIN_QUERY='$query' atuin search --keymap-mode=$keymap_mode$escaped_args -i 2>'$result_file'"
+                sh -c "PATH='$PATH' ATUIN_SESSION='$ATUIN_SESSION' ATUIN_SHELL=fish ATUIN_QUERY='$query' atuin search --keymap-mode=$keymap_mode$escaped_args -i 2>'$result_file'"
             set ATUIN_STATUS $status
 
             if test -f "$result_file"
@@ -132,7 +132,7 @@ function _atuin_search
         # In fish 3.4 and above we can use `"$(some command)"` to keep multiple lines separate;
         # but to support fish 3.3 we need to use `(some command | string collect)`.
         # https://fishshell.com/docs/current/relnotes.html#id24 (fish 3.4 "Notable improvements and fixes")
-        set ATUIN_H (ATUIN_SHELL=fish ATUIN_LOG=error ATUIN_QUERY=(commandline -b) atuin search --keymap-mode=$keymap_mode $argv -i 3>&1 1>&2 2>&3 3>&- | string collect)
+        set ATUIN_H (ATUIN_SHELL=fish ATUIN_QUERY=(commandline -b) atuin search --keymap-mode=$keymap_mode $argv -i 3>&1 1>&2 2>&3 3>&- | string collect)
         set ATUIN_STATUS $pipestatus[1]
     end
 
diff --git a/crates/atuin/src/shell/atuin.nu b/crates/atuin/src/shell/atuin.nu
index c4de1967..fdb87550 100644
--- a/crates/atuin/src/shell/atuin.nu
+++ b/crates/atuin/src/shell/atuin.nu
@@ -48,7 +48,7 @@ let _atuin_pre_execution = {||
         return
     }
     if not ($cmd | str starts-with $ATUIN_KEYBINDING_TOKEN) {
-        $env.ATUIN_HISTORY_ID = (atuin history start -- $cmd | complete | get stdout | str trim)
+        $env.ATUIN_HISTORY_ID = (atuin history start --hook -- $cmd | complete | get stdout | str trim)
         _atuin_osc133_command_executed
     }
 }
@@ -59,15 +59,12 @@ let _atuin_pre_prompt = {||
         return
     }
     _atuin_osc133_command_finished $last_exit
-    with-env { ATUIN_LOG: error } {
-        if (version).minor >= 104 or (version).major > 0 {
-            job spawn {
-                ^atuin history end $'--exit=($env.LAST_EXIT_CODE)' -- $env.ATUIN_HISTORY_ID | complete
-            } | ignore
-        } else {
-            do { atuin history end $'--exit=($last_exit)' -- $env.ATUIN_HISTORY_ID } | complete
-        }
-
+    if (version).minor >= 104 or (version).major > 0 {
+        job spawn {
+            ^atuin history end --hook $'--exit=($env.LAST_EXIT_CODE)' -- $env.ATUIN_HISTORY_ID | complete
+        } | ignore
+    } else {
+        do { atuin history end --hook $'--exit=($last_exit)' -- $env.ATUIN_HISTORY_ID } | complete
     }
     hide-env -i ATUIN_HISTORY_ID
 }
@@ -77,7 +74,7 @@ def _atuin_search_cmd [...flags: string] {
         [
             $ATUIN_KEYBINDING_TOKEN,
             ([
-                `with-env { ATUIN_LOG: error, ATUIN_QUERY: (commandline), ATUIN_SHELL: nu } {`,
+                `with-env { ATUIN_QUERY: (commandline), ATUIN_SHELL: nu } {`,
                     ([
                         'let output = (run-external atuin search',
                         ($flags | append [--interactive] | each {|e| $'"($e)"'}),
@@ -95,7 +92,7 @@ def _atuin_search_cmd [...flags: string] {
         [
             $ATUIN_KEYBINDING_TOKEN,
             ([
-                `with-env { ATUIN_LOG: error, ATUIN_QUERY: (commandline) } {`,
+                `with-env { ATUIN_QUERY: (commandline) } {`,
                     'commandline edit',
                     '(run-external atuin search',
                         ($flags | append [--interactive] | each {|e| $'"($e)"'}),
diff --git a/crates/atuin/src/shell/atuin.ps1 b/crates/atuin/src/shell/atuin.ps1
index 431ee2c3..fa059977 100644
--- a/crates/atuin/src/shell/atuin.ps1
+++ b/crates/atuin/src/shell/atuin.ps1
@@ -77,7 +77,7 @@ New-Module -Name Atuin -ScriptBlock {
                 # Fire and forget the atuin history end command to avoid blocking the shell during a potential sync.
                 $process = New-Object System.Diagnostics.Process
                 $process.StartInfo.FileName = "atuin"
-                $process.StartInfo.Arguments = "history end --exit=$exitCode $durationArg -- $script:atuinHistoryId"
+                $process.StartInfo.Arguments = "history end --hook --exit=$exitCode $durationArg -- $script:atuinHistoryId"
                 $process.StartInfo.UseShellExecute = $false
                 $process.StartInfo.CreateNoWindow = $true
                 $process.StartInfo.RedirectStandardInput = $true
@@ -117,7 +117,7 @@ New-Module -Name Atuin -ScriptBlock {
         # This makes it unreliable, so we go through an environment variable, which should always be consistent across versions.
         try {
             $env:ATUIN_COMMAND_LINE = $line
-            $script:atuinHistoryId = atuin history start --command-from-env
+            $script:atuinHistoryId = atuin history start --hook --command-from-env
         }
         catch {
             # Ignore errors to avoid breaking the shell, see above.
diff --git a/crates/atuin/src/shell/atuin.xsh b/crates/atuin/src/shell/atuin.xsh
index a0283402..501d02d5 100644
--- a/crates/atuin/src/shell/atuin.xsh
+++ b/crates/atuin/src/shell/atuin.xsh
@@ -14,7 +14,7 @@ if "ATUIN_SESSION" not in ${...} or ${...}.get("ATUIN_SHLVL", "") != ${...}.get(
 def _atuin_precommand(cmd: str):
     cmd = cmd.rstrip("\n")
     try:
-        $ATUIN_HISTORY_ID = $(atuin history start -- @(cmd) 2>@(os.devnull)).rstrip("\n")
+        $ATUIN_HISTORY_ID = $(atuin history start --hook -- @(cmd) 2>@(os.devnull)).rstrip("\n")
     except:
         $ATUIN_HISTORY_ID = ""
 
@@ -27,12 +27,12 @@ def _atuin_postcommand(cmd: str, rtn: int, out, ts):
     duration = ts[1] - ts[0]
     # Duration is float representing seconds, but atuin expects integer of nanoseconds
     nanos = round(duration * 10 ** 9)
-    with ${...}.swap(ATUIN_LOG="error"):
-        # This causes the entire .xonshrc to be re-executed, which is incredibly slow
-        # This happens when using a subshell and using output redirection at the same time
-        # For more details, see https://github.com/xonsh/xonsh/issues/5224
-        # (atuin history end --exit @(rtn) -- $ATUIN_HISTORY_ID &) > /dev/null 2>&1
-        atuin history end --exit @(rtn) --duration @(nanos) -- $ATUIN_HISTORY_ID > @(os.devnull) 2>&1
+
+    # This causes the entire .xonshrc to be re-executed, which is incredibly slow
+    # This happens when using a subshell and using output redirection at the same time
+    # For more details, see https://github.com/xonsh/xonsh/issues/5224
+    # (atuin history end --hook --exit @(rtn) -- $ATUIN_HISTORY_ID &) > /dev/null 2>&1
+    atuin history end --hook --exit @(rtn) --duration @(nanos) -- $ATUIN_HISTORY_ID > @(os.devnull) 2>&1
     del $ATUIN_HISTORY_ID
 
 
diff --git a/crates/atuin/src/shell/atuin.zsh b/crates/atuin/src/shell/atuin.zsh
index f8461006..26436139 100644
--- a/crates/atuin/src/shell/atuin.zsh
+++ b/crates/atuin/src/shell/atuin.zsh
@@ -70,7 +70,7 @@ __atuin_osc133_wrap_prompt() {
 
 _atuin_preexec() {
     local id
-    id=$(atuin history start -- "$1" 2>/dev/null)
+    id=$(atuin history start --hook -- "$1" 2>/dev/null)
     export ATUIN_HISTORY_ID="$id"
     __atuin_osc133_command_executed
     __atuin_preexec_time=${EPOCHREALTIME-}
@@ -89,7 +89,7 @@ _atuin_precmd() {
     fi
 
     __atuin_osc133_command_finished "$EXIT"
-    (ATUIN_LOG=error atuin history end --exit $EXIT ${duration:+--duration=$duration} -- $ATUIN_HISTORY_ID &) >/dev/null 2>&1
+    (atuin history end --hook --exit $EXIT ${duration:+--duration=$duration} -- $ATUIN_HISTORY_ID >/dev/null 2>&1 &)
     export ATUIN_HISTORY_ID=""
 }
 
@@ -141,7 +141,7 @@ __atuin_search_cmd() {
         popup_width="${ATUIN_TMUX_POPUP_WIDTH:-80%}" # Keep default value anyways
         popup_height="${ATUIN_TMUX_POPUP_HEIGHT:-60%}"
         tmux display-popup -d "$cdir" -w "$popup_width" -h "$popup_height" -E -E -- \
-            sh -c "PATH='$PATH' ATUIN_SESSION='$ATUIN_SESSION' ATUIN_SHELL=zsh ATUIN_LOG=error ATUIN_QUERY='$escaped_query' atuin search $escaped_args -i 2>'$result_file'"
+            sh -c "PATH='$PATH' ATUIN_SESSION='$ATUIN_SESSION' ATUIN_SHELL=zsh ATUIN_QUERY='$escaped_query' atuin search $escaped_args -i 2>'$result_file'"
 
         if [[ -f "$result_file" ]]; then
             cat "$result_file"
@@ -150,7 +150,7 @@ __atuin_search_cmd() {
         __atuin_tmux_popup_cleanup
         trap - EXIT HUP INT TERM
     else
-        ATUIN_SHELL=zsh ATUIN_LOG=error ATUIN_QUERY=$BUFFER atuin search "${search_args[@]}" -i 3>&1 1>&2 2>&3 3>&-
+        ATUIN_SHELL=zsh ATUIN_QUERY=$BUFFER atuin search "${search_args[@]}" -i 3>&1 1>&2 2>&3 3>&-
     fi
 }