diff --git a/docs/ci-integration.md b/docs/ci-integration.md
index b9d526f..5d7253d 100644
--- a/docs/ci-integration.md
+++ b/docs/ci-integration.md
@@ -50,7 +50,18 @@ Checks that fail cause the test to fail. Checks that warn still pass (they're in
 
 ## Running a subset of checks
 
-If certain checks don't apply to your site (for example, you don't serve markdown), limit which checks run in the config:
+To exclude specific checks, use `skipChecks`. For example, a local preview server may not implement the content negotiation or cache headers supplied by your production server:
+
+```yaml
+url: https://docs.example.com
+skipChecks:
+  - content-negotiation
+  - cache-header-hygiene
+```
+
+Both helpers honor `skipChecks`. Excluded checks do not run; the per-check helper logs their results with a `skip` status. Prefer this exclude-list for ongoing CI: checks added in later AFDocs versions still run automatically.
+
+For a deliberately narrow run, use the `checks` include-list instead:
 
 ```yaml
 url: https://docs.example.com
@@ -69,7 +80,12 @@ Checks not in the list show as skipped in the test output.
 ```yaml
 url: https://docs.example.com
 
-# Optional: run only specific checks (omit to run all 28)
+# Optional: skip specific checks (run everything else, including future checks)
+# skipChecks:
+#   - content-negotiation
+#   - cache-header-hygiene
+
+# Optional: run only specific checks
 # checks:
 #   - llms-txt-exists
 #   - llms-txt-valid
@@ -208,7 +224,7 @@ on:
       - 'docs/**'
 ```
 
-One limitation to plan around: `skipChecks` is currently honored by the CLI and ignored by the vitest helpers ([afdocs#133](https://github.com/agent-ecosystem/afdocs/issues/133)). Until that is fixed, run the localhost target through `afdocs check --config agent-docs.local.yml` rather than the helpers.
+The CLI and both vitest helpers honor `skipChecks`.
 
 AFDocs checks its own docs site this way; the two workflows are [agent-docs.yml](https://github.com/agent-ecosystem/afdocs/blob/main/.github/workflows/agent-docs.yml) and [agent-docs-live.yml](https://github.com/agent-ecosystem/afdocs/blob/main/.github/workflows/agent-docs-live.yml).
 
diff --git a/src/helpers/vitest-runner.ts b/src/helpers/vitest-runner.ts
index e4b8b41..f0146c0 100644
--- a/src/helpers/vitest-runner.ts
+++ b/src/helpers/vitest-runner.ts
@@ -54,6 +54,7 @@ export function describeAgentDocs(
             : undefined;
         const report = await runChecks(config.url, {
           checkIds: config.checks,
+          skipCheckIds: config.skipChecks,
           ...config.options,
           ...(inferredStrategy && { samplingStrategy: inferredStrategy as 'curated' }),
           curatedPages: config.pages,
@@ -104,6 +105,7 @@ export function describeAgentDocsPerCheck(
           : undefined;
       report = await runChecks(config.url, {
         checkIds: config.checks,
+        skipCheckIds: config.skipChecks,
         ...config.options,
         ...(inferredStrategy && { samplingStrategy: inferredStrategy as 'curated' }),
         curatedPages: config.pages,
diff --git a/src/runner.ts b/src/runner.ts
index c0396e0..24d2b76 100644
--- a/src/runner.ts
+++ b/src/runner.ts
@@ -173,7 +173,7 @@ export async function runChecks(
         id: check.id,
         category: check.category,
         status: 'skip',
-        message: 'Check skipped (excluded via --skip-checks)',
+        message: 'Check explicitly skipped',
       };
       storeInPreviousResults = false;
     } else if (
diff --git a/test/integration/dependency-chains.test.ts b/test/integration/dependency-chains.test.ts
index f2ac05b..7e7ae33 100644
--- a/test/integration/dependency-chains.test.ts
+++ b/test/integration/dependency-chains.test.ts
@@ -200,7 +200,7 @@ describe('--skip-checks interaction with dependencies', () => {
     // markdown-url-support should be explicitly skipped
     const mdUrl = report.results.find((r) => r.id === 'markdown-url-support')!;
     expect(mdUrl.status).toBe('skip');
-    expect(mdUrl.message).toContain('--skip-checks');
+    expect(mdUrl.message).toBe('Check explicitly skipped');
 
     // content-negotiation should still run (not affected by skip)
     const cn = report.results.find((r) => r.id === 'content-negotiation')!;
@@ -234,7 +234,7 @@ describe('--skip-checks interaction with dependencies', () => {
 
     const exists = report.results.find((r) => r.id === 'llms-txt-exists')!;
     expect(exists.status).toBe('skip');
-    expect(exists.message).toContain('--skip-checks');
+    expect(exists.message).toBe('Check explicitly skipped');
 
     // The runner does NOT block llms-txt-valid (dep "never ran" from runner's
     // perspective, since --skip-checks results aren't stored in previousResults).
diff --git a/test/unit/helpers/vitest-runner.test.ts b/test/unit/helpers/vitest-runner.test.ts
new file mode 100644
index 0000000..2e9f5b0
--- /dev/null
+++ b/test/unit/helpers/vitest-runner.test.ts
@@ -0,0 +1,101 @@
+import { expect, vi } from 'vitest';
+import type * as Vitest from 'vitest';
+import {
+  describeAgentDocs,
+  describeAgentDocsPerCheck,
+} from '../../../src/helpers/vitest-runner.js';
+import { loadConfig } from '../../../src/helpers/config.js';
+import { runChecks } from '../../../src/runner.js';
+import type { AgentDocsConfig } from '../../../src/types.js';
+
+const { describe, it, beforeEach } = await vi.importActual<typeof Vitest>('vitest');
+
+const { runCallbacks } = vi.hoisted(() => ({
+  runCallbacks: [] as Array<() => Promise<void>>,
+}));
+
+vi.mock('vitest', async (importOriginal) => {
+  const actual = await importOriginal<typeof Vitest>();
+  return {
+    ...actual,
+    describe: (_name: string, register: () => void) => register(),
+    it: (name: string, run: () => Promise<void>) => {
+      if (name === 'should run checks') runCallbacks.push(run);
+    },
+    beforeAll: (run: () => Promise<void>) => runCallbacks.push(run),
+  };
+});
+
+vi.mock('../../../src/helpers/config.js', () => ({ loadConfig: vi.fn() }));
+vi.mock('../../../src/runner.js', () => ({
+  runChecks: vi.fn(async () => ({ results: [] })),
+}));
+
+beforeEach(() => {
+  vi.clearAllMocks();
+  runCallbacks.length = 0;
+});
+
+describe.each([
+  { name: 'describeAgentDocs', helper: describeAgentDocs },
+  { name: 'describeAgentDocsPerCheck', helper: describeAgentDocsPerCheck },
+])('$name', ({ helper }) => {
+  const config: AgentDocsConfig = {
+    url: 'https://docs.example.com',
+    checks: ['llms-txt-exists', 'content-negotiation'],
+    skipChecks: ['content-negotiation'],
+    pages: [
+      'https://docs.example.com/quickstart',
+      { url: 'https://docs.example.com/api/auth', tag: 'api-reference' },
+    ],
+    options: { maxLinksToTest: 5 },
+  };
+
+  it.each(['inline', 'directory', 'default'] as const)(
+    'forwards checks, skipChecks, pages, and options from %s config',
+    async (source) => {
+      vi.mocked(loadConfig).mockResolvedValue(config);
+      const input = source === 'inline' ? config : source === 'directory' ? '/docs' : undefined;
+
+      helper(input);
+      expect(runCallbacks).toHaveLength(1);
+      await runCallbacks[0]();
+
+      expect(runChecks).toHaveBeenCalledExactlyOnceWith(config.url, {
+        checkIds: config.checks,
+        skipCheckIds: config.skipChecks,
+        curatedPages: config.pages,
+        maxLinksToTest: 5,
+        samplingStrategy: 'curated',
+      });
+      if (source === 'inline') {
+        expect(loadConfig).not.toHaveBeenCalled();
+      } else {
+        expect(loadConfig).toHaveBeenCalledExactlyOnceWith(input);
+      }
+    },
+  );
+
+  it('leaves selection and sampling unset when not configured', async () => {
+    helper({ url: config.url });
+    await runCallbacks[0]();
+
+    expect(runChecks).toHaveBeenCalledExactlyOnceWith(config.url, {
+      checkIds: undefined,
+      skipCheckIds: undefined,
+      curatedPages: undefined,
+    });
+  });
+
+  it('preserves an explicit sampling strategy with curated pages', async () => {
+    helper({ ...config, options: { samplingStrategy: 'deterministic' } });
+    await runCallbacks[0]();
+
+    expect(runChecks).toHaveBeenCalledExactlyOnceWith(config.url, {
+      checkIds: config.checks,
+      skipCheckIds: config.skipChecks,
+      curatedPages: config.pages,
+      samplingStrategy: 'deterministic',
+    });
+  });
+});
diff --git a/test/unit/runner.test.ts b/test/unit/runner.test.ts
index 7f75655..96fedda 100644
--- a/test/unit/runner.test.ts
+++ b/test/unit/runner.test.ts
@@ -482,7 +482,7 @@ describe('runner', () => {
     const skipped = report.results.find((r) => r.id === 'llms-txt-valid');
     expect(skipped).toBeDefined();
     expect(skipped?.status).toBe('skip');
-    expect(skipped?.message).toContain('--skip-checks');
+    expect(skipped?.message).toBe('Check explicitly skipped');
 
     // llms-txt-exists should still run (not in skipCheckIds)
     const exists = report.results.find((r) => r.id === 'llms-txt-exists');
@@ -520,7 +520,7 @@ describe('runner', () => {
 
     const exists = report.results.find((r) => r.id === 'llms-txt-exists');
     expect(exists?.status).toBe('skip');
-    expect(exists?.message).toContain('--skip-checks');
+    expect(exists?.message).toBe('Check explicitly skipped');
 
     // llms-txt-valid should run in standalone mode, not cascade-skip
     const valid = report.results.find((r) => r.id === 'llms-txt-valid');
diff --git a/vitest.config.ts b/vitest.config.ts
index c3fc3eb..626a7d8 100644
--- a/vitest.config.ts
+++ b/vitest.config.ts
@@ -7,7 +7,6 @@ export default defineConfig({
     coverage: {
       provider: 'v8',
       include: ['src/**/*.ts'],
-      exclude: ['src/helpers/vitest-runner.ts'],
     },
   },
 });