diff --git a/.changeset/nested-variant-skill-path.md b/.changeset/nested-variant-skill-path.md
new file mode 100644
index 00000000..88c2a4dd
--- /dev/null
+++ b/.changeset/nested-variant-skill-path.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/intent': patch
+---
+
+Fix `intent load` for a skill that ships in a nested copy of a dependency. When a workspace package such as `packages/bar` installed its own version of `@tanstack/query`, and the root `node_modules/@tanstack/query` was a different copy, `list` showed the nested skill but `load` looked for it under `node_modules/@tanstack/query/...` and failed. Intent now uses the `node_modules/<name>/...` path only when that entry is the same copy. Otherwise it reports the project-relative path, such as `packages/bar/node_modules/@tanstack/query/skills/fetching/SKILL.md`. Hoisted installs and pnpm or bun symlinks to the same copy keep their `node_modules/<name>/...` paths.
diff --git a/packages/intent/src/skills/paths.ts b/packages/intent/src/skills/paths.ts
index 7092140a..58f159ed 100644
--- a/packages/intent/src/skills/paths.ts
+++ b/packages/intent/src/skills/paths.ts
@@ -1,4 +1,4 @@
-import { existsSync } from 'node:fs'
+import { realpathSync } from 'node:fs'
 import { join, relative } from 'node:path'
 import { toPosixPath } from '../shared/utils.js'
 import { formatIntentCommand } from '../shared/command-runner.js'
@@ -52,12 +52,19 @@ export function rewriteSkillLoadPaths({
 }): void {
   const topLevelPackageRoot =
     packageName !== '' ? join(projectRoot, 'node_modules', packageName) : ''
-  const hasStableSymlink =
-    topLevelPackageRoot !== '' &&
-    (packageRoot === topLevelPackageRoot || existsSync(topLevelPackageRoot))
+  let matchesTopLevelEntry: boolean
+  try {
+    matchesTopLevelEntry =
+      topLevelPackageRoot !== '' &&
+      (packageRoot === topLevelPackageRoot ||
+        realpathSync.native(topLevelPackageRoot) ===
+          realpathSync.native(packageRoot))
+  } catch {
+    matchesTopLevelEntry = false
+  }
 
   for (const skill of skills) {
-    if (hasStableSymlink) {
+    if (matchesTopLevelEntry) {
       const relFromPackage = toPosixPath(relative(packageRoot, skill.path))
       skill.path = `node_modules/${packageName}/${relFromPackage}`
     } else {
diff --git a/packages/intent/tests/core.test.ts b/packages/intent/tests/core.test.ts
index 6be0edde..a075290d 100644
--- a/packages/intent/tests/core.test.ts
+++ b/packages/intent/tests/core.test.ts
@@ -968,6 +968,41 @@ describe('loadIntentSkill', () => {
     )
   })
 
+  it('loads a nested dependency copy when the root has a different copy', () => {
+    const barDir = join(root, 'packages', 'bar')
+    writeJson(join(root, 'package.json'), {
+      name: 'test-monorepo',
+      private: true,
+      workspaces: ['packages/*'],
+    })
+    writeJson(join(barDir, 'package.json'), {
+      name: 'bar',
+      dependencies: {
+        '@tanstack/query': '5.0.0',
+      },
+    })
+    writeJson(
+      join(root, 'node_modules', '@tanstack', 'query', 'package.json'),
+      {
+        name: '@tanstack/query',
+        version: '4.0.0',
+      },
+    )
+    writeInstalledIntentPackage(barDir, {
+      name: '@tanstack/query',
+      version: '5.0.0',
+      skillName: 'fetching',
+      description: 'Query data fetching patterns',
+    })
+
+    const result = loadIntentSkill('@tanstack/query#fetching', { cwd: root })
+
+    expect(result.version).toBe('5.0.0')
+    expect(result.path).toBe(
+      'packages/bar/node_modules/@tanstack/query/skills/fetching/SKILL.md',
+    )
+  })
+
   it('rewrites relative markdown destinations in loaded content', () => {
     const pkgDir = join(root, 'node_modules', '@tanstack', 'query')
     const skillDir = join(pkgDir, 'skills', 'fetching')
diff --git a/packages/intent/tests/skill-paths.test.ts b/packages/intent/tests/skill-paths.test.ts
index 4759608a..86c9cbf5 100644
--- a/packages/intent/tests/skill-paths.test.ts
+++ b/packages/intent/tests/skill-paths.test.ts
@@ -1,4 +1,4 @@
-import { mkdirSync, mkdtempSync, rmSync } from 'node:fs'
+import { mkdirSync, mkdtempSync, rmSync, symlinkSync } from 'node:fs'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
 import { afterEach, describe, expect, it } from 'vitest'
@@ -79,7 +79,7 @@ describe('skill path helpers', () => {
     expect(isStableLoadPath('')).toBe(false)
   })
 
-  it('rewrites to stable node_modules load paths when a top-level package path exists', () => {
+  it('rewrites to stable node_modules load paths when the package root is the top-level entry', () => {
     const root = tempRoot()
     const packageRoot = join(root, 'node_modules', '@tanstack', 'query')
     const skillPath = join(packageRoot, 'skills', 'core', 'SKILL.md')
@@ -98,6 +98,68 @@ describe('skill path helpers', () => {
     )
   })
 
+  it('keeps the project-relative path when the top-level package is a different copy', () => {
+    const root = tempRoot()
+    mkdirSync(join(root, 'node_modules', '@tanstack', 'query'), {
+      recursive: true,
+    })
+    const packageRoot = join(
+      root,
+      'packages',
+      'bar',
+      'node_modules',
+      '@tanstack',
+      'query',
+    )
+    const skillPath = join(packageRoot, 'skills', 'core', 'SKILL.md')
+    mkdirSync(join(packageRoot, 'skills', 'core'), { recursive: true })
+    const skills = [skill(skillPath)]
+
+    rewriteSkillLoadPaths({
+      packageName: '@tanstack/query',
+      packageRoot,
+      projectRoot: root,
+      skills,
+    })
+
+    expect(skills[0]!.path).toBe(
+      'packages/bar/node_modules/@tanstack/query/skills/core/SKILL.md',
+    )
+  })
+
+  it('rewrites a symlinked store copy to the top-level link that targets it', () => {
+    const root = tempRoot()
+    const packageRoot = join(
+      root,
+      'node_modules',
+      '.pnpm',
+      '@tanstack+query@5.0.0',
+      'node_modules',
+      '@tanstack',
+      'query',
+    )
+    const skillPath = join(packageRoot, 'skills', 'core', 'SKILL.md')
+    mkdirSync(join(packageRoot, 'skills', 'core'), { recursive: true })
+    mkdirSync(join(root, 'node_modules', '@tanstack'))
+    symlinkSync(
+      packageRoot,
+      join(root, 'node_modules', '@tanstack', 'query'),
+      'dir',
+    )
+    const skills = [skill(skillPath)]
+
+    rewriteSkillLoadPaths({
+      packageName: '@tanstack/query',
+      packageRoot,
+      projectRoot: root,
+      skills,
+    })
+
+    expect(skills[0]!.path).toBe(
+      'node_modules/@tanstack/query/skills/core/SKILL.md',
+    )
+  })
+
   it('does not invent stable top-level load paths for pnpm-internal package paths', () => {
     const root = tempRoot()
     const packageRoot = join(