diff --git a/src/commands/helpers.ts b/src/commands/helpers.ts
index 922ca75..44b31b9 100644
--- a/src/commands/helpers.ts
+++ b/src/commands/helpers.ts
@@ -141,6 +141,7 @@ export async function mergeAndClose(branch: string, opts?: { squash?: boolean; f
 
   try {
     await vm.ensure((msg) => { spin.text = msg })
+    if (session) await vm.setActivity(session.worktree, branch)
     await resolveConflicts(conflicts, root, (file) => { spin.text = `Resolving ${file}` })
 
     if (opts?.squash) {
@@ -154,6 +155,8 @@ export async function mergeAndClose(branch: string, opts?: { squash?: boolean; f
     spin.fail(message)
     await git.abortMerge(root)
     process.exit(1)
+  } finally {
+    if (session) await vm.clearActivity(session.worktree, branch)
   }
 
   if (session) await teardownSession(root, branch, session.worktree)
diff --git a/src/commands/rebase.ts b/src/commands/rebase.ts
index ff7b220..c1012f2 100644
--- a/src/commands/rebase.ts
+++ b/src/commands/rebase.ts
@@ -33,6 +33,7 @@ export async function action(branch: string) {
 
   try {
     await vm.ensure((msg) => { resolveSpin.text = msg })
+    await vm.setActivity(worktree, branch)
 
     let round = 1
     while (conflicts.length > 0) {
@@ -53,5 +54,7 @@ export async function action(branch: string) {
     resolveSpin.fail(String((err as Error).message ?? err))
     await git.rebaseAbort(worktree)
     process.exit(1)
+  } finally {
+    await vm.clearActivity(worktree, branch)
   }
 }
diff --git a/src/vm.ts b/src/vm.ts
index bb7476c..bcfde9d 100644
--- a/src/vm.ts
+++ b/src/vm.ts
@@ -358,6 +358,12 @@ export async function isClaudeActive(worktree: string, branch: string): Promise<
   }
 }
 
+/** Set the activity marker for a worktree (e.g. during conflict resolution). */
+export async function setActivity(worktree: string, branch: string): Promise<void> {
+  const file = `${dirname(worktree)}/.activity-${branch}`
+  await Bun.write(file, "active\n")
+}
+
 /** Remove the activity marker file for a worktree. */
 export async function clearActivity(worktree: string, branch: string): Promise<void> {
   const file = `${dirname(worktree)}/.activity-${branch}`