diff --git a/plugins/multipart/test/dynamic-option.test.ts b/plugins/multipart/test/dynamic-option.test.ts
index 770e8e15a5..edfb8b109a 100644
--- a/plugins/multipart/test/dynamic-option.test.ts
+++ b/plugins/multipart/test/dynamic-option.test.ts
@@ -21,7 +21,7 @@ describe('test/dynamic-option.test.ts', () => {
   });
 
   afterAll(async () => {
-    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
   });
   afterAll(() => app.close());
   afterAll(() => server.close());
diff --git a/plugins/multipart/test/enable-pathToRegexpModule.test.ts b/plugins/multipart/test/enable-pathToRegexpModule.test.ts
index 88b2ffe543..fb5fe2fe18 100644
--- a/plugins/multipart/test/enable-pathToRegexpModule.test.ts
+++ b/plugins/multipart/test/enable-pathToRegexpModule.test.ts
@@ -23,7 +23,7 @@ describe.skip('test/enable-pathToRegexpModule.test.ts', () => {
     host = 'http://127.0.0.1:' + server.address().port;
   });
   afterAll(async () => {
-    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
   });
   afterAll(() => app.close());
   afterAll(() => server.close());
diff --git a/plugins/multipart/test/file-mode-limit-filesize-per-request.test.ts b/plugins/multipart/test/file-mode-limit-filesize-per-request.test.ts
index 9f82f78f4a..0f38283c06 100644
--- a/plugins/multipart/test/file-mode-limit-filesize-per-request.test.ts
+++ b/plugins/multipart/test/file-mode-limit-filesize-per-request.test.ts
@@ -22,7 +22,7 @@ describe('test/file-mode-limit-filesize-per-request.test.ts', () => {
     host = 'http://127.0.0.1:' + server.address().port;
   });
   afterAll(async () => {
-    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
   });
   afterAll(() => app.close());
   afterAll(() => server.close());
diff --git a/plugins/multipart/test/file-mode.test.ts b/plugins/multipart/test/file-mode.test.ts
index f419482052..7d5952afad 100644
--- a/plugins/multipart/test/file-mode.test.ts
+++ b/plugins/multipart/test/file-mode.test.ts
@@ -28,7 +28,7 @@ describe('test/file-mode.test.ts', () => {
     host = 'http://127.0.0.1:' + server.address().port;
   });
   afterAll(async () => {
-    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+    await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
   });
   afterAll(() => app.close());
   afterAll(() => server.close());
diff --git a/plugins/multipart/test/stream-mode-with-filematch-glob.test.ts b/plugins/multipart/test/stream-mode-with-filematch-glob.test.ts
index cae967574f..cf8da45de9 100644
--- a/plugins/multipart/test/stream-mode-with-filematch-glob.test.ts
+++ b/plugins/multipart/test/stream-mode-with-filematch-glob.test.ts
@@ -26,7 +26,7 @@ describe('test/stream-mode-with-filematch-glob.test.ts', () => {
   });
   afterAll(async () => {
     try {
-      await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+      await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
     } catch (err) {
       console.error(err);
     }
diff --git a/plugins/multipart/test/stream-mode-with-filematch.test.ts b/plugins/multipart/test/stream-mode-with-filematch.test.ts
index 7dd35e67e3..da7134659c 100644
--- a/plugins/multipart/test/stream-mode-with-filematch.test.ts
+++ b/plugins/multipart/test/stream-mode-with-filematch.test.ts
@@ -26,7 +26,7 @@ describe('test/stream-mode-with-filematch.test.ts', () => {
   });
   afterAll(async () => {
     try {
-      await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+      await fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
     } catch (err) {
       console.error(err);
     }
diff --git a/plugins/multipart/test/ts.test.ts b/plugins/multipart/test/ts.test.ts
index 487db2366e..5308441027 100644
--- a/plugins/multipart/test/ts.test.ts
+++ b/plugins/multipart/test/ts.test.ts
@@ -25,7 +25,7 @@ describe('test/ts.test.ts', () => {
     host = 'http://127.0.0.1:' + server.address().port;
   });
   afterAll(() => {
-    return fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true });
+    return fs.rm(app.config.multipart.tmpdir, { force: true, recursive: true, maxRetries: 3 });
   });
   afterAll(() => app.close());
   afterAll(() => server.close());
diff --git a/tools/scripts/test/stop.test.ts b/tools/scripts/test/stop.test.ts
index 9f30b74622..eb9c62d2ff 100644
--- a/tools/scripts/test/stop.test.ts
+++ b/tools/scripts/test/stop.test.ts
@@ -8,7 +8,7 @@ import { mm, restore } from 'mm';
 import { describe, it, beforeAll, afterAll, beforeEach, afterEach, expect } from 'vitest';
 
 import { isWindows } from '../src/helper.ts';
-import { cleanup, replaceWeakRefMessage, type Coffee } from './utils.ts';
+import { cleanup, replaceWeakRefMessage, waitFor, type Coffee } from './utils.ts';
 
 const __dirname = import.meta.dirname;
 
@@ -45,7 +45,9 @@ describe('test/stop.test.ts', () => {
       ]) as Coffee;
       app.debug();
       app.expect('code', 0);
-      await scheduler.wait(waitTime);
+      // Poll until the app reports it has started instead of a fixed delay: a 2-worker
+      // egg app can take well over a second to boot on a loaded CI runner.
+      await waitFor(() => app.stdout, /custom-framework started on http:\/\/127\.0\.0\.1:\d+/);
 
       expect(replaceWeakRefMessage(app.stderr)).toBe('');
       expect(app.stdout).toMatch(/custom-framework started on http:\/\/127\.0\.0\.1:\d+/);
@@ -155,7 +157,8 @@ describe('test/stop.test.ts', () => {
       ]) as Coffee;
       // app.debug();
       app.expect('code', 0);
-      await scheduler.wait(waitTime);
+      // Poll until the app reports it has started (see note above).
+      await waitFor(() => app.stdout, /custom-framework started on http:\/\/127\.0\.0\.1:\d+/);
 
       expect(replaceWeakRefMessage(app.stderr)).toBe('');
       expect(app.stdout).toMatch(/custom-framework started on http:\/\/127\.0\.0\.1:\d+/);
@@ -314,7 +317,8 @@ describe('test/stop.test.ts', () => {
       app.debug();
       app.expect('code', 0);
 
-      await scheduler.wait(waitTime);
+      // Poll until the app reports it has started (see note above).
+      await waitFor(() => app.stdout, /http:\/\/127\.0\.0\.1:\d+/);
 
       // assert.equal(replaceWeakRefMessage(app.stderr), '');
       expect(app.stdout).toMatch(/http:\/\/127\.0\.0\.1:\d+/);
@@ -332,7 +336,13 @@ describe('test/stop.test.ts', () => {
       killer.debug();
       killer.expect('code', 0);
       await killer.end();
-      await scheduler.wait(waitTime);
+      // Poll until the app logs its shutdown instead of a fixed delay. On Windows the
+      // SIGTERM signal is not handled (no shutdown log), so keep a fixed settle there.
+      if (isWindows) {
+        await scheduler.wait(waitTime);
+      } else {
+        await waitFor(() => app.stdout, /\[master] master is killed by signal SIGTERM, closing/);
+      }
 
       // make sure is kill not auto exist
       expect(app.stdout).not.toMatch(/exist by env/);
@@ -356,7 +366,13 @@ describe('test/stop.test.ts', () => {
       killer.expect('code', 0);
 
       // await killer.end();
-      await scheduler.wait(waitTime);
+      // Poll until the app has fully exited (master exits last, after workers/agent),
+      // instead of a fixed delay. On Windows the signal is not handled, so settle fixed.
+      if (isWindows) {
+        await scheduler.wait(waitTime);
+      } else {
+        await waitFor(() => app.stdout, /\[master] exit with code:0/);
+      }
 
       // make sure is kill not auto exist
       expect(app.stdout).not.toMatch(/exist by env/);
diff --git a/tools/scripts/test/utils.ts b/tools/scripts/test/utils.ts
index 79ffaf6867..4d491d3242 100644
--- a/tools/scripts/test/utils.ts
+++ b/tools/scripts/test/utils.ts
@@ -55,3 +55,19 @@ export function replaceWeakRefMessage(stderr: string) {
   }
   return stderr;
 }
+
+/**
+ * Poll until `getText()` matches `pattern`, up to `timeout` ms (default 10s),
+ * checking every 100ms. Returns as soon as it matches, and resolves anyway on
+ * timeout so the caller's own `expect(...).toMatch(...)` still produces a useful
+ * diff. Use this instead of a fixed `scheduler.wait(n)` before asserting on a
+ * forked process's stdout: a loaded CI runner may not have finished booting (or
+ * shutting down) within `n`, which is the classic source of these flaky timeouts.
+ */
+export async function waitFor(getText: () => string, pattern: RegExp, timeout = 10000): Promise<void> {
+  const deadline = Date.now() + timeout;
+  while (!pattern.test(getText())) {
+    if (Date.now() >= deadline) return;
+    await scheduler.wait(100);
+  }
+}