diff --git a/.changeset/icy-loops-act.md b/.changeset/icy-loops-act.md
new file mode 100644
index 0000000..30d8324
--- /dev/null
+++ b/.changeset/icy-loops-act.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/intent': patch
+---
+
+Fix maintainer review discovering skills inside hidden agent directories
diff --git a/packages/intent/src/maintainer/existing.ts b/packages/intent/src/maintainer/existing.ts
index 0434ca0..967e65d 100644
--- a/packages/intent/src/maintainer/existing.ts
+++ b/packages/intent/src/maintainer/existing.ts
@@ -3,7 +3,7 @@ import { existsSync } from 'node:fs'
 import { basename, dirname, relative } from 'node:path'
 import { resolveProjectContext } from '../core/project-context.js'
 import { resolveWorkspacePackages } from '../setup/workspace-patterns.js'
-import { parseFrontmatter } from '../shared/utils.js'
+import { isDefaultSkillPath, parseFrontmatter } from '../shared/utils.js'
 import { stringList } from './add.js'
 import {
   isObject,
@@ -76,9 +76,7 @@ export function findExistingSkills(
       (path) =>
         basename(path) === 'SKILL.md' &&
         /(^|\/)skills\//.test(path) &&
-        !path
-          .split('/')
-          .some((part) => part.startsWith('.') || part === 'node_modules') &&
+        isDefaultSkillPath(path) &&
         !registered.has(path),
     )
     .sort()
diff --git a/packages/intent/src/review/review.ts b/packages/intent/src/review/review.ts
index 77c9b0d..106413d 100644
--- a/packages/intent/src/review/review.ts
+++ b/packages/intent/src/review/review.ts
@@ -14,7 +14,7 @@ import {
 import { basename, dirname, join, relative, resolve } from 'node:path'
 import { parse as parseYaml } from 'yaml'
 import { resolveProjectContext } from '../core/project-context.js'
-import { parseFrontmatter } from '../shared/utils.js'
+import { isDefaultSkillPath, parseFrontmatter } from '../shared/utils.js'
 
 type Snapshot = Record<string, string | null>
 type Outcome = 'updated' | 'no-change' | 'out-of-scope' | 'unresolved'
@@ -565,7 +565,7 @@ export function createReview(cwd: string, baseRef?: string): ReviewReport {
   const skillFiles = files.filter(
     (path) =>
       basename(path) === 'SKILL.md' &&
-      (/(^|\/)skills\//.test(path) ||
+      ((/(^|\/)skills\//.test(path) && isDefaultSkillPath(path)) ||
         customRoots.some((dir) => path.startsWith(`${dir}/`)) ||
         declaredSkills.has(path) ||
         state?.items[`skill:${path}`]),
diff --git a/packages/intent/src/shared/utils.ts b/packages/intent/src/shared/utils.ts
index d998558..8e47165 100644
--- a/packages/intent/src/shared/utils.ts
+++ b/packages/intent/src/shared/utils.ts
@@ -58,6 +58,19 @@ export function toPosixPath(p: string): string {
   return p.split(sep).join('/')
 }
 
+/**
+ * Check whether a skill path belongs to the default skill discovery tree.
+ *
+ * Hidden directories and node_modules are excluded from default discovery,
+ * while explicitly declared or custom-root skills can still be handled by
+ * their respective discovery paths.
+ */
+export function isDefaultSkillPath(path: string): boolean {
+  return !path
+    .split('/')
+    .some((part) => part.startsWith('.') || part === 'node_modules')
+}
+
 export interface FsIdentityResolver {
   (path: string): string
   /**
diff --git a/packages/intent/tests/review.test.ts b/packages/intent/tests/review.test.ts
index 7741909..bcf07b2 100644
--- a/packages/intent/tests/review.test.ts
+++ b/packages/intent/tests/review.test.ts
@@ -147,7 +147,71 @@ it('does not classify shipped meta skills or unrelated agent instructions as lib
   accept()
   expect(createReview(root).items).toEqual([])
 })
+it('ignores hidden agent directories during default skill discovery', () => {
+  write(
+    '.claude/skills/deploy/SKILL.md',
+    '---\nname: deploy\ndescription: Deploy safely\n---\nDeploy guidance.\n',
+  )
+  write(
+    '.cursor/skills/review/SKILL.md',
+    '---\nname: review\ndescription: Review safely\n---\nReview guidance.\n',
+  )
+  write(
+    '.agents/skills/hidden/SKILL.md',
+    '---\nname: hidden\ndescription: Hidden guidance\n---\nHidden guidance.\n',
+  )
+
+  git('add', '.')
+  git('commit', '-qm', 'hidden agent skills')
 
+  expect(createReview(root).items.map((item) => item.id)).toEqual([
+    'skill:skills/request/SKILL.md',
+  ])
+})
+it('retains a hidden skill through review state without explicit declaration or custom root', () => {
+  const skillPath = '.agents/skills/hidden/SKILL.md'
+
+  write(
+    skillPath,
+    '---\nname: hidden\nsources: [src/hidden.ts]\n---\nHidden guidance.\n',
+  )
+  write('src/hidden.ts', 'export const hidden = true\n')
+
+  planningRecords('_artifacts')
+  write(
+    '_artifacts/skill_tree.yaml',
+    `library: { name: library }\nskills: [{path: ${skillPath}}]\n`,
+  )
+
+  git('add', '.')
+  git('commit', '-qm', 'record hidden skill')
+
+  const initial = createReview(root)
+
+  expect(initial.items.map((item) => item.id)).toContain(`skill:${skillPath}`)
+
+  expect(
+    initial.items.find((item) => item.id === `skill:${skillPath}`)?.problems,
+  ).toEqual([])
+
+  accept(initial)
+
+  write(
+    '_artifacts/skill_tree.yaml',
+    'library: { name: library }\nskills: []\n',
+  )
+
+  write('src/hidden.ts', 'export const hidden = false\n')
+
+  const retained = createReview(root)
+  const retainedSkill = retained.items.find(
+    (item) => item.id === `skill:${skillPath}`,
+  )
+
+  expect(retainedSkill).toBeDefined()
+  expect(retainedSkill?.problems).toEqual([])
+  expect(retainedSkill?.changedFiles).toContain('src/hidden.ts')
+})
 it('reviews a repository-root skill without including its own review state', () => {
   renameSync(join(root, 'skills/request/SKILL.md'), join(root, 'SKILL.md'))
   planningRecords('_artifacts')