diff --git a/mlf-cli/src/generate/mlf.rs b/mlf-cli/src/generate/mlf.rs
index 83310fe..0c1c0ed 100644
--- a/mlf-cli/src/generate/mlf.rs
+++ b/mlf-cli/src/generate/mlf.rs
@@ -51,7 +51,7 @@ pub enum MlfGenerateError {
     },
 }
 
-pub fn run(input_patterns: Vec<String>, output_dir: Option<PathBuf>) -> Result<(), MlfGenerateError> {
+pub fn run(input_patterns: Vec<String>, output_dir: Option<PathBuf>, flat: bool) -> Result<(), MlfGenerateError> {
     let current_dir = std::env::current_dir().map_err(|source| MlfGenerateError::WriteOutput {
         path: "current directory".to_string(),
         source,
@@ -147,19 +147,24 @@ pub fn run(input_patterns: Vec<String>, output_dir: Option<PathBuf>) -> Result<(
                 message: "Missing 'id' field in lexicon".to_string(),
             })?;
 
-        // Create output path from namespace
-        let mut output_path = output_dir.clone();
-        for segment in namespace.split('.') {
-            output_path.push(segment);
-        }
-        if let Err(source) = std::fs::create_dir_all(&output_path.parent().unwrap()) {
-            errors.push((
-                file_path.display().to_string(),
-                format!("Failed to create directory: {}", source),
-            ));
-            continue;
-        }
-        output_path.set_extension("mlf");
+        let output_path = if flat {
+            output_dir.join(format!("{}.mlf", namespace))
+        } else {
+            // Create output path from namespace
+            let mut path = output_dir.clone();
+            for segment in namespace.split('.') {
+                path.push(segment);
+            }
+            if let Err(source) = std::fs::create_dir_all(&path.parent().unwrap()) {
+                errors.push((
+                        file_path.display().to_string(),
+                        format!("Failed to create directory: {}", source),
+                ));
+                continue;
+            }
+            path.set_extension("mlf");
+            path
+        };
 
         if let Err(source) = std::fs::write(&output_path, mlf_content) {
             errors.push((
diff --git a/mlf-cli/src/main.rs b/mlf-cli/src/main.rs
index 4575387..ed7a7d5 100644
--- a/mlf-cli/src/main.rs
+++ b/mlf-cli/src/main.rs
@@ -109,6 +109,9 @@ enum GenerateCommands {
 
         #[arg(short, long, help = "Output directory. If omitted, uses first mlf output from mlf.toml")]
         output: Option<PathBuf>,
+
+        #[arg(long, help = "Use flat file structure (e.g., app.bsky.post.json)")]
+        flat: bool,
     },
 }
 
@@ -133,8 +136,8 @@ async fn main() {
             Some(GenerateCommands::Code { generator, input, output, root, flat }) => {
                 generate::code::run(generator, input, output, root, flat).into_diagnostic()
             }
-            Some(GenerateCommands::Mlf { input, output }) => {
-                generate::mlf::run(input, output).into_diagnostic()
+            Some(GenerateCommands::Mlf { input, output, flat }) => {
+                generate::mlf::run(input, output, flat).into_diagnostic()
             }
             None => {
                 // Run all outputs from mlf.toml