diff --git a/crates/core/src/project.rs b/crates/core/src/project.rs
index 731e815d..797ead89 100644
--- a/crates/core/src/project.rs
+++ b/crates/core/src/project.rs
@@ -140,6 +140,21 @@ pub struct SessionMeta {
 }
 
 impl SessionMeta {
+    /// Whether `other` works in the worktree this session owns. A fork keeps
+    /// the source's cwd without the `worktree` ownership marker, so the cwd
+    /// decides as well as the branch.
+    pub fn shares_worktree_with(&self, other: &SessionMeta) -> bool {
+        let Some(worktree) = &self.worktree else {
+            return false;
+        };
+        other.id != self.id
+            && (other.cwd.starts_with(&self.cwd)
+                || other
+                    .worktree
+                    .as_ref()
+                    .is_some_and(|other| other.branch == worktree.branch))
+    }
+
     /// The key [`Settings::provider_color`] resolves this thread's color from:
     /// a user profile id, an ACP agent (`acp:<id>`), or the built-in
     /// [`provider_key`]. A user profile is its own provider to the user even
@@ -540,6 +555,30 @@ mod tests {
         assert_eq!(acp.provider_color_key(), "acp:gemini");
     }
 
+    #[test]
+    fn worktree_is_shared_by_a_fork_in_its_cwd_but_not_by_a_sibling_directory() {
+        let mut owner = SessionMeta::new(ProviderKind::Codex, PathBuf::from("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/wt/source"), None);
+        owner.worktree = Some(WorktreeInfo {
+            root_project_path: PathBuf::from("/repo"),
+            base: "main".into(),
+            branch: "tcode/source".into(),
+        });
+        let fork = SessionMeta::new(ProviderKind::Codex, owner.cwd.clone(), None);
+        let nested = SessionMeta::new(ProviderKind::Codex, owner.cwd.join("crates/core"), None);
+        let sibling = SessionMeta::new(ProviderKind::Codex, PathBuf::from("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/wt/source-2"), None);
+        let checkout = SessionMeta::new(ProviderKind::Codex, PathBuf::from("/repo"), None);
+
+        assert!(owner.shares_worktree_with(&fork));
+        assert!(owner.shares_worktree_with(&nested));
+        assert!(!owner.shares_worktree_with(&sibling));
+        assert!(!owner.shares_worktree_with(&checkout));
+        assert!(!owner.shares_worktree_with(&owner));
+        assert!(
+            !fork.shares_worktree_with(&owner),
+            "a fork owns no worktree"
+        );
+    }
+
     fn candidates(
         sessions: &[SessionMeta],
         now: u64,
diff --git a/crates/runtime/src/app/sessions.rs b/crates/runtime/src/app/sessions.rs
index daad0547..92d09119 100644
--- a/crates/runtime/src/app/sessions.rs
+++ b/crates/runtime/src/app/sessions.rs
@@ -974,10 +974,20 @@ impl AppState {
         }
         self.close_orchestrator_children(session_id, cx);
         let worktree_remove = meta.as_ref().and_then(|meta| {
-            (remove_worktree && meta.worktree.is_some()).then(|| {
-                let worktree = meta.worktree.as_ref().unwrap();
-                (worktree.root_project_path.clone(), meta.cwd.clone())
-            })
+            let worktree = meta.worktree.as_ref().filter(|_| remove_worktree)?;
+            let shared = self
+                .sessions
+                .iter()
+                .chain(self.residents.live.values().map(|session| &session.meta))
+                .any(|other| meta.shares_worktree_with(other));
+            if shared {
+                log::info!(
+                    "keeping worktree {} in use by another thread",
+                    meta.cwd.display()
+                );
+                return None;
+            }
+            Some((worktree.root_project_path.clone(), meta.cwd.clone()))
         });
         self.settings.last_visited.remove(session_id);
         self.settings
@@ -1110,16 +1120,24 @@ impl AppState {
             .is_some_and(|&visited| meta.updated_at > visited)
     }
 
-    /// Remove app-owned worktrees whose session is absent from the loaded store.
+    /// Remove app-owned worktrees that no session in the loaded store owns or
+    /// works in.
     pub(crate) fn recover_orphaned_worktrees(&self, cx: &mut HostCx) {
         let known_ids = self
             .sessions
             .iter()
             .map(|session| session.id.clone())
             .collect();
+        let cwds: Vec<_> = self
+            .sessions
+            .iter()
+            .map(|session| session.cwd.clone())
+            .collect();
         let host_cx = cx.clone();
         HostCx::spawn_detached(cx, async move {
-            let summary = host_cx.unblock(move || cleanup_orphans(&known_ids)).await;
+            let summary = host_cx
+                .unblock(move || cleanup_orphans(&known_ids, &cwds))
+                .await;
             if !summary.removed.is_empty() || !summary.skipped.is_empty() {
                 log::info!(
                     "worktree orphan recovery removed {}, left {}",
diff --git a/crates/services/src/worktree.rs b/crates/services/src/worktree.rs
index e7d62e7e..2722c68e 100644
--- a/crates/services/src/worktree.rs
+++ b/crates/services/src/worktree.rs
@@ -398,15 +398,20 @@ fn worktrees_root() -> PathBuf {
         })
 }
 
-/// Remove old app-owned worktrees whose directory names are not known session ids.
+/// Remove old, clean app-owned worktrees that no known session owns or works in.
 ///
 /// Tests and isolated processes may set `TCODE_WORKTREES_DIR`; production falls
 /// back to `~/.tcode/worktrees`. Fresh unknown entries are presumed live and
-/// preserved for at least [`ORPHAN_MIN_AGE`].
-pub fn cleanup_orphans(known_session_ids: &HashSet<String>) -> CleanupSummary {
+/// preserved for at least [`ORPHAN_MIN_AGE`]. Removal is never forced: a
+/// worktree the user kept on delete may hold uncommitted work.
+pub fn cleanup_orphans(
+    known_session_ids: &HashSet<String>,
+    session_cwds: &[PathBuf],
+) -> CleanupSummary {
     cleanup_orphans_at(
         &worktrees_root(),
         known_session_ids,
+        session_cwds,
         SystemTime::now(),
         ORPHAN_MIN_AGE,
     )
@@ -415,6 +420,7 @@ pub fn cleanup_orphans(known_session_ids: &HashSet<String>) -> CleanupSummary {
 fn cleanup_orphans_at(
     worktrees: &Path,
     known_session_ids: &HashSet<String>,
+    session_cwds: &[PathBuf],
     now: SystemTime,
     minimum_age: Duration,
 ) -> CleanupSummary {
@@ -436,7 +442,10 @@ fn cleanup_orphans_at(
         let is_directory = entry
             .file_type()
             .is_ok_and(|kind| kind.is_dir() && !kind.is_symlink());
-        if known_session_ids.contains(&session_id) || !is_directory {
+        if known_session_ids.contains(&session_id)
+            || session_cwds.iter().any(|cwd| cwd.starts_with(&path))
+            || !is_directory
+        {
             continue;
         }
         let modified = match entry.metadata().and_then(|metadata| metadata.modified()) {
@@ -481,12 +490,7 @@ fn cleanup_orphans_at(
         };
         let output = crate::process::command("git")
             .current_dir(&removal_root)
-            .args([
-                "worktree",
-                "remove",
-                "--force",
-                &registered.to_string_lossy(),
-            ])
+            .args(["worktree", "remove", &registered.to_string_lossy()])
             .output();
         match output {
             Ok(output) if output.status.success() => {
@@ -994,34 +998,48 @@ mod tests {
         let orphan = provision_for_test(&root, "orphan", &worktrees).path;
         let modified = std::fs::metadata(&orphan).unwrap().modified().unwrap();
         let kept = provision_for_test(&root, "kept", &worktrees).path;
+        // A deleted source whose fork still runs in its worktree.
+        let forked = provision_for_test(&root, "deleted-source", &worktrees).path;
+        // Deleted with "Keep worktree" while holding uncommitted work.
+        let dirty = provision_for_test(&root, "kept-on-delete", &worktrees).path;
+        std::fs::write(dirty.join("notes.txt"), "uncommitted\n").unwrap();
         let known = HashSet::from(["kept".to_string()]);
+        let cwds = [forked.clone()];
 
-        let fresh = cleanup_orphans_at(&worktrees, &known, modified, ORPHAN_MIN_AGE);
+        let fresh = cleanup_orphans_at(&worktrees, &known, &cwds, modified, ORPHAN_MIN_AGE);
         assert!(fresh.removed.is_empty());
-        assert_eq!(fresh.skipped.as_slice(), std::slice::from_ref(&orphan));
+        let mut skipped = fresh.skipped;
+        skipped.sort();
+        assert_eq!(skipped, [dirty.clone(), orphan.clone()]);
         assert!(orphan.exists());
 
         let old = cleanup_orphans_at(
             &worktrees,
             &known,
+            &cwds,
             modified + ORPHAN_MIN_AGE + Duration::from_secs(1),
             ORPHAN_MIN_AGE,
         );
         assert_eq!(old.removed.as_slice(), std::slice::from_ref(&orphan));
-        assert!(old.skipped.is_empty());
+        assert_eq!(old.skipped.as_slice(), std::slice::from_ref(&dirty));
         assert!(!orphan.exists());
         assert!(kept.join("tracked.txt").exists());
+        assert!(forked.join("tracked.txt").exists());
+        assert!(dirty.join("notes.txt").exists());
         let unrelated = worktrees.join("unregistered");
         std::fs::create_dir(&unrelated).unwrap();
         let modified = std::fs::metadata(&unrelated).unwrap().modified().unwrap();
         let summary = cleanup_orphans_at(
             &worktrees,
             &known,
+            &cwds,
             modified + ORPHAN_MIN_AGE + Duration::from_secs(1),
             ORPHAN_MIN_AGE,
         );
         assert!(summary.removed.is_empty());
-        assert_eq!(summary.skipped.as_slice(), std::slice::from_ref(&unrelated));
+        let mut skipped = summary.skipped;
+        skipped.sort();
+        assert_eq!(skipped, [dirty, unrelated.clone()]);
         assert!(unrelated.exists());
         let _ = std::fs::remove_dir_all(temp);
     }
diff --git a/crates/ui/src/store/mod.rs b/crates/ui/src/store/mod.rs
index 31bb9e63..1833de3a 100644
--- a/crates/ui/src/store/mod.rs
+++ b/crates/ui/src/store/mod.rs
@@ -2824,16 +2824,15 @@ impl WorkspaceStore {
             .iter()
             .find(|meta| meta.id == session_id)?;
         let worktree = meta.worktree.clone()?;
-        let shared = self.index_replica.0.iter().any(|meta| {
-            meta.id != session_id
-                && meta
-                    .worktree
-                    .as_ref()
-                    .is_some_and(|other| other.branch == worktree.branch)
-        }) || self
-            .index_summary
-            .archived_worktree_branches
-            .contains(&worktree.branch);
+        let shared = self
+            .index_replica
+            .0
+            .iter()
+            .any(|other| meta.shares_worktree_with(other))
+            || self
+                .index_summary
+                .archived_worktree_branches
+                .contains(&worktree.branch);
         (!shared).then_some(worktree)
     }
 }