diff --git a/packages/opencode/src/project/instance-store.ts b/packages/opencode/src/project/instance-store.ts
index 1f513fb1b..ccac93ae1 100644
--- a/packages/opencode/src/project/instance-store.ts
+++ b/packages/opencode/src/project/instance-store.ts
@@ -19,6 +19,7 @@ export interface Interface {
   readonly load: (input: LoadInput) => Effect.Effect<InstanceContext>
   readonly reload: (input: LoadInput) => Effect.Effect<InstanceContext>
   readonly dispose: (ctx: InstanceContext) => Effect.Effect<void>
+  readonly disposeDirectory: (directory: string) => Effect.Effect<void>
   readonly disposeAll: () => Effect.Effect<void>
   readonly provide: <A, E, R>(input: LoadInput, effect: Effect.Effect<A, E, R>) => Effect.Effect<A, E, R>
 }
@@ -151,6 +152,15 @@ export const layer: Layer.Layer<Service, never, Project.Service | InstanceBootst
       yield* disposeEntry(ctx.directory, entry, ctx).pipe(Effect.asVoid)
     })
 
+    const disposeDirectory = Effect.fn("InstanceStore.disposeDirectory")(function* (input: string) {
+      const directory = AppFileSystem.resolve(input)
+      const entry = cache.get(directory)
+      if (!entry) return
+      const exit = yield* Deferred.await(entry.deferred).pipe(Effect.exit)
+      if (Exit.isFailure(exit)) return yield* removeEntry(directory, entry).pipe(Effect.asVoid)
+      yield* disposeEntry(directory, entry, exit.value).pipe(Effect.asVoid)
+    })
+
     const disposeAllOnce = Effect.fnUntraced(function* () {
       yield* Effect.logInfo("disposing all instances")
       yield* Effect.forEach(
@@ -185,6 +195,7 @@ export const layer: Layer.Layer<Service, never, Project.Service | InstanceBootst
       load,
       reload,
       dispose,
+      disposeDirectory,
       disposeAll,
       provide,
     })
diff --git a/packages/opencode/src/worktree/index.ts b/packages/opencode/src/worktree/index.ts
index e02e7a3bd..76884eb60 100644
--- a/packages/opencode/src/worktree/index.ts
+++ b/packages/opencode/src/worktree/index.ts
@@ -395,6 +395,9 @@ export const layer: Layer.Layer<
 
       const directory = yield* canonical(input.directory)
 
+      // Bootstrapped worktrees may hold file handles, which must be released before removal on Windows.
+      if (directory !== (yield* canonical(ctx.worktree))) yield* store.disposeDirectory(directory)
+
       const list = yield* git(["worktree", "list", "--porcelain"], { cwd: ctx.worktree })
       if (list.code !== 0) {
         return yield* new RemoveFailedError({ message: list.stderr || list.text || "Failed to read git worktrees" })
diff --git a/packages/opencode/test/project/worktree.test.ts b/packages/opencode/test/project/worktree.test.ts
index 688b818be..35e598443 100644
--- a/packages/opencode/test/project/worktree.test.ts
+++ b/packages/opencode/test/project/worktree.test.ts
@@ -5,10 +5,8 @@ import { CrossSpawnSpawner } from "@opencode-ai/core/cross-spawn-spawner"
 import { Cause, Deferred, Effect, Exit, Fiber, Layer } from "effect"
 import { GlobalBus, type GlobalEvent } from "../../src/bus/global"
 import { Git } from "../../src/git"
-import { InstanceRef } from "../../src/effect/instance-ref"
-import { InstanceRuntime } from "../../src/project/instance-runtime"
 import { Worktree } from "../../src/worktree"
-import { disposeAllInstances, provideInstance, TestInstance } from "../fixture/fixture"
+import { disposeAllInstances, TestInstance } from "../fixture/fixture"
 import { testEffect } from "../lib/effect"
 
 const it = testEffect(
@@ -41,11 +39,6 @@ const waitReady = Effect.fn("WorktreeTest.waitReady")(function* () {
 const removeCreatedWorktree = (directory: string) =>
   Effect.gen(function* () {
     const svc = yield* Worktree.Service
-    const ctx = yield* Effect.gen(function* () {
-      return yield* InstanceRef
-    }).pipe(provideInstance(directory))
-    if (!ctx) return yield* Effect.die(new Error("missing test instance"))
-    yield* Effect.promise(() => InstanceRuntime.disposeInstance(ctx))
     const ok = yield* svc.remove({ directory })
     if (!ok) return yield* Effect.fail(new Error(`failed to remove worktree ${directory}`))
   })