diff --git a/src/cmd/amend.rs b/src/cmd/amend.rs
index 74303de..4670181 100644
--- a/src/cmd/amend.rs
+++ b/src/cmd/amend.rs
@@ -66,16 +66,15 @@ pub fn run(message: Option<&str>, all: bool) -> Result<()> {
     let current_root = git::repo_root()?;
 
     for child_name in &children {
-        // Guard FIRST — before extracting old_parent_head.
-        if let Ok(Some(_wt_path)) = git::branch_checked_out_elsewhere(child_name, &current_root) {
-            ui::info(&format!("Skipped `{child_name}` (in worktree)"));
-            continue;
-        }
-
         let old_parent_head = state.get_branch(child_name)?.parent_head.clone();
 
         let sp = ui::spinner(&format!("Restacking `{child_name}`..."));
-        let outcome = git::rebase_onto(&current_head, &old_parent_head, child_name)?;
+        let outcome = git::rebase_onto_for_branch(
+            &current_head,
+            &old_parent_head,
+            child_name,
+            &current_root,
+        )?;
         sp.finish_and_clear();
 
         match outcome {
diff --git a/src/cmd/commit.rs b/src/cmd/commit.rs
index e7baad7..d00e318 100644
--- a/src/cmd/commit.rs
+++ b/src/cmd/commit.rs
@@ -71,17 +71,11 @@ pub fn run(
     let mut restacked_count = 0;
 
     for child in &children {
-        // Guard FIRST — before extracting old_base (avoids unused-variable warning when skipping).
-        if let Ok(Some(_wt_path)) = git::branch_checked_out_elsewhere(child, &current_root) {
-            ui::info(&format!("Skipped `{child}` (in worktree)"));
-            continue;
-        }
-
         let meta = state.get_branch(child)?;
         let old_base = meta.parent_head.clone();
 
         ui::info(&format!("Restacking `{child}`..."));
-        match git::rebase_onto(&new_head, &old_base, child)? {
+        match git::rebase_onto_for_branch(&new_head, &old_base, child, &current_root)? {
             git::RebaseOutcome::RebasingComplete => {}
             git::RebaseOutcome::Conflict(conflict) => {
                 // Save progress so the user can fix conflicts and continue with `ez restack`.
diff --git a/src/cmd/merge.rs b/src/cmd/merge.rs
index ef1c5b2..14e3ef2 100644
--- a/src/cmd/merge.rs
+++ b/src/cmd/merge.rs
@@ -111,13 +111,13 @@ fn merge_branch(
             continue;
         }
 
-        if let Ok(Some(_wt_path)) = git::branch_checked_out_elsewhere(branch_name, &current_root) {
-            ui::warn(&format!("Skipped `{branch_name}` (in worktree)"));
-            continue;
-        }
-
         let sp = ui::spinner(&format!("Restacking `{branch_name}` onto `{parent}`..."));
-        let outcome = git::rebase_onto(&current_parent_tip, &stored_parent_head, branch_name)?;
+        let outcome = git::rebase_onto_for_branch(
+            &current_parent_tip,
+            &stored_parent_head,
+            branch_name,
+            &current_root,
+        )?;
         sp.finish_and_clear();
 
         match outcome {
diff --git a/src/cmd/move_branch.rs b/src/cmd/move_branch.rs
index 5ad2bae..1b7918b 100644
--- a/src/cmd/move_branch.rs
+++ b/src/cmd/move_branch.rs
@@ -95,11 +95,6 @@ pub fn run(onto: Option<&str>) -> Result<()> {
     let current_root = git::repo_root()?;
 
     for child_name in &children {
-        if let Ok(Some(_wt_path)) = git::branch_checked_out_elsewhere(child_name, &current_root) {
-            ui::warn(&format!("Skipped `{child_name}` (in worktree)"));
-            continue;
-        }
-
         let child = state.get_branch(child_name)?;
         let child_parent_head = child.parent_head.clone();
 
@@ -108,7 +103,8 @@ pub fn run(onto: Option<&str>) -> Result<()> {
         }
 
         let sp = ui::spinner(&format!("Restacking `{child_name}` onto `{current}`..."));
-        let outcome = git::rebase_onto(&new_tip, &child_parent_head, child_name)?;
+        let outcome =
+            git::rebase_onto_for_branch(&new_tip, &child_parent_head, child_name, &current_root)?;
         sp.finish_and_clear();
 
         match outcome {
diff --git a/src/cmd/restack.rs b/src/cmd/restack.rs
index a7606ce..6c0909b 100644
--- a/src/cmd/restack.rs
+++ b/src/cmd/restack.rs
@@ -29,7 +29,6 @@ pub fn run() -> Result<()> {
 
     let order = state.topo_order();
     let mut restacked = 0;
-    let mut skipped = 0;
 
     for branch_name in &order {
         let meta = state.get_branch(branch_name)?;
@@ -42,18 +41,16 @@ pub fn run() -> Result<()> {
             continue;
         }
 
-        // Guard: skip branches checked out in another worktree.
-        if let Ok(Some(_wt_path)) = git::branch_checked_out_elsewhere(branch_name, &current_root) {
-            ui::warn(&format!("Skipped `{branch_name}` (in worktree)"));
-            skipped += 1;
-            continue;
-        }
-
-        // Branch is stale — rebase onto the new parent tip.
+        // Branch is stale — rebase onto the new parent tip (in its worktree if needed).
         let before_sha = git::rev_parse(branch_name).unwrap_or_default();
 
         let sp = ui::spinner(&format!("Restacking `{branch_name}` onto `{parent}`..."));
-        let outcome = git::rebase_onto(&current_parent_tip, &stored_parent_head, branch_name)?;
+        let outcome = git::rebase_onto_for_branch(
+            &current_parent_tip,
+            &stored_parent_head,
+            branch_name,
+            &current_root,
+        )?;
         sp.finish_and_clear();
 
         match outcome {
@@ -73,7 +70,7 @@ pub fn run() -> Result<()> {
                         ui::info(&format!(
                             "Dropping {redundant_count} redundant commit(s) from `{branch_name}` (already in `{parent}`)",
                         ));
-                        match git::rebase(&parent, branch_name) {
+                        match git::rebase_for_branch(&parent, branch_name, &current_root) {
                             Ok(true) => {
                                 ui::info(&format!(
                                     "Dropped redundant commits from `{branch_name}`"
@@ -121,7 +118,7 @@ pub fn run() -> Result<()> {
 
     state.save()?;
 
-    if restacked == 0 && skipped == 0 {
+    if restacked == 0 {
         ui::info("All branches are up to date — nothing to restack");
     }
 
diff --git a/src/cmd/sync.rs b/src/cmd/sync.rs
index a852a6e..8a96aa9 100644
--- a/src/cmd/sync.rs
+++ b/src/cmd/sync.rs
@@ -397,16 +397,15 @@ fn run_sync_inner(force: bool) -> Result<()> {
             continue;
         }
 
-        // Guard: skip branches checked out in another worktree.
-        if let Ok(Some(_wt_path)) = git::branch_checked_out_elsewhere(branch_name, &original_root) {
-            ui::warn(&format!("Skipped `{branch_name}` (in worktree)"));
-            continue;
-        }
-
         let before_sha = git::rev_parse(branch_name).unwrap_or_default();
 
         let sp = ui::spinner(&format!("Restacking `{branch_name}` onto `{parent}`..."));
-        let outcome = git::rebase_onto(&current_parent_tip, &stored_parent_head, branch_name)?;
+        let outcome = git::rebase_onto_for_branch(
+            &current_parent_tip,
+            &stored_parent_head,
+            branch_name,
+            &original_root,
+        )?;
         sp.finish_and_clear();
 
         match outcome {
@@ -426,7 +425,7 @@ fn run_sync_inner(force: bool) -> Result<()> {
                         ui::info(&format!(
                             "Dropping {redundant_count} redundant commit(s) from `{branch_name}` (already in `{parent}`)",
                         ));
-                        match git::rebase(&parent, branch_name) {
+                        match git::rebase_for_branch(&parent, branch_name, &original_root) {
                             Ok(true) => {
                                 ui::info(&format!(
                                     "Dropped redundant commits from `{branch_name}`"
diff --git a/src/git.rs b/src/git.rs
index cf44c43..361c227 100644
--- a/src/git.rs
+++ b/src/git.rs
@@ -322,22 +322,65 @@ fn fetch_args(remote: &str) -> [&str; 3] {
     ["fetch", "--progress", remote]
 }
 
-pub fn rebase_onto(new_base: &str, old_base: &str, branch: &str) -> Result<RebaseOutcome> {
-    let (success, _, stderr) =
-        run_git_with_status(&["rebase", "--onto", new_base, old_base, branch])?;
+fn rebase_onto_impl(
+    scope: Option<&str>,
+    new_base: &str,
+    old_base: &str,
+    branch: Option<&str>,
+) -> Result<RebaseOutcome> {
+    let mut args: Vec<&str> = Vec::new();
+    if let Some(dir) = scope {
+        args.extend(["-C", dir]);
+    }
+    args.extend(["rebase", "--onto", new_base, old_base]);
+    if let Some(branch_name) = branch {
+        args.push(branch_name);
+    }
+
+    let (success, _, stderr) = run_git_with_status(&args)?;
+
+    let mut abort_args: Vec<&str> = Vec::new();
+    if let Some(dir) = scope {
+        abort_args.extend(["-C", dir]);
+    }
+    abort_args.extend(["rebase", "--abort"]);
+
     if success {
         Ok(RebaseOutcome::RebasingComplete)
     } else if stderr.contains("CONFLICT") || stderr.contains("conflict") {
         // Abort the rebase so we leave the repo in a clean state
-        let _ = run_git(&["rebase", "--abort"]);
+        let _ = run_git(&abort_args);
         Ok(RebaseOutcome::Conflict(parse_rebase_conflict(&stderr)))
     } else {
         // Some other rebase failure — try to abort and report
-        let _ = run_git(&["rebase", "--abort"]);
+        let _ = run_git(&abort_args);
         bail!(EzError::GitError(stderr));
     }
 }
 
+pub fn rebase_onto(new_base: &str, old_base: &str, branch: &str) -> Result<RebaseOutcome> {
+    rebase_onto_impl(None, new_base, old_base, Some(branch))
+}
+
+/// Rebase the branch checked out in `dir` onto `new_base`, dropping commits up to `old_base`.
+pub fn rebase_onto_at(dir: &str, new_base: &str, old_base: &str) -> Result<RebaseOutcome> {
+    rebase_onto_impl(Some(dir), new_base, old_base, None)
+}
+
+/// Rebase `branch` onto `new_base`, running the rebase in its worktree when checked out elsewhere.
+pub fn rebase_onto_for_branch(
+    new_base: &str,
+    old_base: &str,
+    branch: &str,
+    current_root: &str,
+) -> Result<RebaseOutcome> {
+    if let Some(wt_path) = branch_checked_out_elsewhere(branch, current_root)? {
+        rebase_onto_at(&wt_path, new_base, old_base)
+    } else {
+        rebase_onto(new_base, old_base, branch)
+    }
+}
+
 fn parse_rebase_conflict(stderr: &str) -> RebaseConflict {
     RebaseConflict {
         conflicting_files: parse_conflicting_files(stderr),
@@ -376,14 +419,29 @@ fn parse_conflicting_files(stderr: &str) -> Vec<String> {
     files.into_iter().collect()
 }
 
-/// Plain `git rebase <upstream> <branch>` — uses git's built-in patch-id detection
-/// to auto-skip commits already applied upstream. Returns true on success.
-pub fn rebase(upstream: &str, branch: &str) -> Result<bool> {
-    let (success, _, stderr) = run_git_with_status(&["rebase", upstream, branch])?;
+fn rebase_impl(scope: Option<&str>, upstream: &str, branch: Option<&str>) -> Result<bool> {
+    let mut args: Vec<&str> = Vec::new();
+    if let Some(dir) = scope {
+        args.extend(["-C", dir]);
+    }
+    args.push("rebase");
+    args.push(upstream);
+    if let Some(branch_name) = branch {
+        args.push(branch_name);
+    }
+
+    let (success, _, stderr) = run_git_with_status(&args)?;
+
+    let mut abort_args: Vec<&str> = Vec::new();
+    if let Some(dir) = scope {
+        abort_args.extend(["-C", dir]);
+    }
+    abort_args.extend(["rebase", "--abort"]);
+
     if success {
         Ok(true)
     } else {
-        let _ = run_git(&["rebase", "--abort"]);
+        let _ = run_git(&abort_args);
         if stderr.contains("CONFLICT") || stderr.contains("conflict") {
             Ok(false)
         } else {
@@ -392,6 +450,26 @@ pub fn rebase(upstream: &str, branch: &str) -> Result<bool> {
     }
 }
 
+/// Plain `git rebase <upstream> <branch>` — uses git's built-in patch-id detection
+/// to auto-skip commits already applied upstream. Returns true on success.
+pub fn rebase(upstream: &str, branch: &str) -> Result<bool> {
+    rebase_impl(None, upstream, Some(branch))
+}
+
+/// Rebase the branch checked out in `dir` onto `upstream`.
+pub fn rebase_at(dir: &str, upstream: &str) -> Result<bool> {
+    rebase_impl(Some(dir), upstream, None)
+}
+
+/// Rebase `branch` onto `upstream`, running the rebase in its worktree when checked out elsewhere.
+pub fn rebase_for_branch(upstream: &str, branch: &str, current_root: &str) -> Result<bool> {
+    if let Some(wt_path) = branch_checked_out_elsewhere(branch, current_root)? {
+        rebase_at(&wt_path, upstream)
+    } else {
+        rebase(upstream, branch)
+    }
+}
+
 pub fn fast_forward_merge(remote_ref: &str) -> Result<()> {
     run_git(&["merge", "--ff-only", remote_ref])?;
     Ok(())
@@ -876,6 +954,31 @@ CONFLICT (modify/delete): src/old.ts deleted in HEAD and modified in abc123.\n";
         );
     }
 
+    #[test]
+    fn rebase_onto_at_uses_worktree_directory() {
+        let _guard = take_env_lock();
+        let log_dir = crate::test_support::temp_dir("git-rebase-at");
+        let log_path = log_dir.join("calls.log");
+        let fake_dir = install_fake_bin(
+            "git-rebase-at-bin",
+            "git",
+            &format!(
+                r#"#!/bin/sh
+echo "$@" >> "{}"
+exit 0
+"#,
+                log_path.display()
+            ),
+        );
+        let _path = PathGuard::install(&fake_dir);
+
+        rebase_onto_at("/repo/.worktrees/feat-a", "main", "old-base").expect("rebase at");
+        assert_eq!(
+            std::fs::read_to_string(log_path).expect("log"),
+            "-C /repo/.worktrees/feat-a rebase --onto main old-base\n"
+        );
+    }
+
     #[test]
     fn rebase_onto_aborts_and_returns_conflict_details() {
         let _guard = take_env_lock();