diff --git a/supacodeTests/GitWtWorktreeEntryTests.swift b/supacodeTests/GitWtWorktreeEntryTests.swift
--- a/supacodeTests/GitWtWorktreeEntryTests.swift
+++ b/supacodeTests/GitWtWorktreeEntryTests.swift
@@ -23,7 +23,7 @@
       GitWtWorktreeEntry(branch: "(bare)", path: "/tmp/repo.git", head: "", isBare: true),
       GitWtWorktreeEntry(branch: "main", path: "/tmp/worktree", head: "abc123", isBare: false),
     ]
-    let filtered = GitWtWorktreeEntry.filteringBare(entries)
+    let filtered = entries.filter { !$0.isBare }
     #expect(filtered.count == 1)
     #expect(filtered.first?.branch == "main")
   }
diff --git a/supacode/Clients/Git/GitClient.swift b/supacode/Clients/Git/GitClient.swift
--- a/supacode/Clients/Git/GitClient.swift
+++ b/supacode/Clients/Git/GitClient.swift
@@ -67,9 +67,8 @@
       return []
     }
     let data = Data(trimmed.utf8)
-    let entries = GitWtWorktreeEntry.filteringBare(
-      try JSONDecoder().decode([GitWtWorktreeEntry].self, from: data)
-    )
+    let entries = try JSONDecoder().decode([GitWtWorktreeEntry].self, from: data)
+      .filter { !$0.isBare }
     let worktreeEntries = entries.enumerated().map { index, entry in
       let worktreeURL = URL(fileURLWithPath: entry.path).standardizedFileURL
       let name = entry.branch.isEmpty ? worktreeURL.lastPathComponent : entry.branch
@@ -575,7 +574,4 @@
     case isBare = "is_bare"
   }
 
-  static func filteringBare(_ entries: [GitWtWorktreeEntry]) -> [GitWtWorktreeEntry] {
-    entries.filter { !$0.isBare }
-  }
 }
diff --git a/supacode/Features/RepositorySettings/Reducer/RepositorySettingsFeature.swift b/supacode/Features/RepositorySettings/Reducer/RepositorySettingsFeature.swift
--- a/supacode/Features/RepositorySettings/Reducer/RepositorySettingsFeature.swift
+++ b/supacode/Features/RepositorySettings/Reducer/RepositorySettingsFeature.swift
@@ -59,9 +59,20 @@
         }
 
       case .settingsLoaded(let settings, let isBareRepository):
-        state.settings = settings
+        var updatedSettings = settings
+        if isBareRepository {
+          updatedSettings.copyIgnoredOnWorktreeCreate = false
+          updatedSettings.copyUntrackedOnWorktreeCreate = false
+        }
+        state.settings = updatedSettings
         state.isBareRepository = isBareRepository
-        return .none
+        guard isBareRepository, updatedSettings != settings else { return .none }
+        let rootURL = state.rootURL
+        let repositorySettingsClient = repositorySettingsClient
+        return .run { send in
+          repositorySettingsClient.save(updatedSettings, rootURL)
+          await send(.delegate(.settingsChanged(rootURL)))
+        }
 
       case .branchDataLoaded(let branches, let defaultBaseRef):
         state.defaultWorktreeBaseRef = defaultBaseRef
@@ -107,6 +118,7 @@
         }
 
       case .setCopyIgnoredOnWorktreeCreate(let isEnabled):
+        guard !state.isBareRepository else { return .none }
         state.settings.copyIgnoredOnWorktreeCreate = isEnabled
         let settings = state.settings
         let rootURL = state.rootURL
@@ -117,6 +129,7 @@
         }
 
       case .setCopyUntrackedOnWorktreeCreate(let isEnabled):
+        guard !state.isBareRepository else { return .none }
         state.settings.copyUntrackedOnWorktreeCreate = isEnabled
         let settings = state.settings
         let rootURL = state.rootURL
diff --git a/supacode/Features/Settings/Views/RepositorySettingsView.swift b/supacode/Features/Settings/Views/RepositorySettingsView.swift
--- a/supacode/Features/Settings/Views/RepositorySettingsView.swift
+++ b/supacode/Features/Settings/Views/RepositorySettingsView.swift
@@ -46,6 +46,7 @@
             set: { store.send(.setCopyIgnoredOnWorktreeCreate($0)) }
           )
         )
+        .disabled(store.isBareRepository)
         Toggle(
           "Copy untracked files to new worktrees",
           isOn: Binding(
@@ -53,6 +54,7 @@
             set: { store.send(.setCopyUntrackedOnWorktreeCreate($0)) }
           )
         )
+        .disabled(store.isBareRepository)
         if store.isBareRepository {
           Text("Copy flags are ignored for bare repositories.")
             .foregroundStyle(.secondary)