diff --git a/.changeset/tangy-plants-hunt.md b/.changeset/tangy-plants-hunt.md
new file mode 100644
index 0000000..9a5bb83
--- /dev/null
+++ b/.changeset/tangy-plants-hunt.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/intent': patch
+---
+
+Fix transitive skill discovery under pnpm's isolated linker. Skills shipped by a transitive dependency of a skill-bearing direct dependency were not discovered… Each package's dependencies are now resolved from its realpath, where pnpm resolution succeeds. Hoisted (npm/yarn/bun) layouts are unaffected.
diff --git a/packages/intent/src/discovery/walk.ts b/packages/intent/src/discovery/walk.ts
index d9b89d9..6709af0 100644
--- a/packages/intent/src/discovery/walk.ts
+++ b/packages/intent/src/discovery/walk.ts
@@ -58,6 +58,8 @@ export function createDependencyWalker(opts: CreateDependencyWalkerOptions) {
   }
 
   function walkDeps(pkgDir: string, pkgName: string): void {
+    // Resolve from the realpath: a pnpm symlink path can't resolve store-only
+    // transitive deps, and walkVisited dedups on realpath so no later retry.
     const pkgKey = opts.getFsIdentity(pkgDir)
     if (walkVisited.has(pkgKey)) return
     walkVisited.add(pkgKey)
@@ -70,7 +72,7 @@ export function createDependencyWalker(opts: CreateDependencyWalkerOptions) {
       return
     }
 
-    walkDepsOf(pkgJson, pkgDir)
+    walkDepsOf(pkgJson, pkgKey)
   }
 
   function walkKnownPackages(): void {
diff --git a/packages/intent/tests/scanner.test.ts b/packages/intent/tests/scanner.test.ts
index 23ede7b..711141d 100644
--- a/packages/intent/tests/scanner.test.ts
+++ b/packages/intent/tests/scanner.test.ts
@@ -194,6 +194,173 @@ describe('scanForIntents', () => {
     expect(result.packages[0]!.name).toBe('my-lib')
   })
 
+  it('discovers transitive skills of a skill-bearing direct dep under pnpm isolated linker (#153)', () => {
+    // pnpm isolated layout: a store-only transitive dep (start-core) reached
+    // only through its skill-bearing parent's (react-start) store dir.
+    writeFileSync(join(root, 'pnpm-lock.yaml'), '')
+    writeJson(join(root, 'package.json'), {
+      name: 'consumer',
+      version: '1.0.0',
+      dependencies: { '@scope/react-start': '1.0.0' },
+    })
+
+    const pnpmDir = join(root, 'node_modules', '.pnpm')
+
+    const startCoreStore = createDir(
+      pnpmDir,
+      '@scope+start-core@1.0.0',
+      'node_modules',
+      '@scope',
+      'start-core',
+    )
+    writeJson(join(startCoreStore, 'package.json'), {
+      name: '@scope/start-core',
+      version: '1.0.0',
+      intent: { version: 1, repo: 'scope/start-core', docs: 'docs/' },
+    })
+    writeSkillMd(createDir(startCoreStore, 'skills', 'start-core'), {
+      name: 'start-core',
+      description: 'Start core skill',
+      type: 'core',
+    })
+
+    const reactStartStore = createDir(
+      pnpmDir,
+      '@scope+react-start@1.0.0',
+      'node_modules',
+      '@scope',
+      'react-start',
+    )
+    writeJson(join(reactStartStore, 'package.json'), {
+      name: '@scope/react-start',
+      version: '1.0.0',
+      intent: { version: 1, repo: 'scope/react-start', docs: 'docs/' },
+      dependencies: { '@scope/start-core': '1.0.0' },
+    })
+    writeSkillMd(createDir(reactStartStore, 'skills', 'react-start'), {
+      name: 'react-start',
+      description: 'React start skill',
+      type: 'core',
+    })
+
+    // start-core symlinked as a sibling inside react-start's store dir only.
+    createDir(pnpmDir, '@scope+react-start@1.0.0', 'node_modules', '@scope')
+    symlinkSync(
+      startCoreStore,
+      join(
+        pnpmDir,
+        '@scope+react-start@1.0.0',
+        'node_modules',
+        '@scope',
+        'start-core',
+      ),
+    )
+
+    // react-start hoisted to the top-level node_modules; start-core is not.
+    createDir(root, 'node_modules', '@scope')
+    symlinkSync(
+      reactStartStore,
+      join(root, 'node_modules', '@scope', 'react-start'),
+    )
+
+    const result = scanForIntents(root)
+
+    const names = result.packages.map((p) => p.name)
+    expect(names).toContain('@scope/react-start')
+    expect(names).toContain('@scope/start-core')
+
+    const startCore = result.packages.find(
+      (p) => p.name === '@scope/start-core',
+    )
+    expect(startCore!.skills.map((s) => s.name)).toContain('start-core')
+
+    // One installed version must not be reported as a version conflict.
+    expect(result.conflicts).toEqual([])
+  })
+
+  it('discovers transitive skills when the dep resolves through a second symlink hop (#153 residual risk)', () => {
+    // The transitive dep is reached through two symlink hops; realpathSync must
+    // collapse the whole chain, not just one hop.
+    writeFileSync(join(root, 'pnpm-lock.yaml'), '')
+    writeJson(join(root, 'package.json'), {
+      name: 'consumer',
+      version: '1.0.0',
+      dependencies: { '@scope/react-start': '1.0.0' },
+    })
+
+    const pnpmDir = join(root, 'node_modules', '.pnpm')
+
+    const startCoreReal = createDir(
+      pnpmDir,
+      '@scope+start-core@1.0.0',
+      'node_modules',
+      '@scope',
+      'start-core',
+    )
+    writeJson(join(startCoreReal, 'package.json'), {
+      name: '@scope/start-core',
+      version: '1.0.0',
+      intent: { version: 1, repo: 'scope/start-core', docs: 'docs/' },
+    })
+    writeSkillMd(createDir(startCoreReal, 'skills', 'start-core'), {
+      name: 'start-core',
+      description: 'Start core skill',
+      type: 'core',
+    })
+
+    // Intermediate symlink hop: a separate link that targets the real store dir.
+    const intermediateScope = createDir(root, '.intermediate', '@scope')
+    const intermediateStartCore = join(intermediateScope, 'start-core')
+    symlinkSync(startCoreReal, intermediateStartCore)
+
+    const reactStartStore = createDir(
+      pnpmDir,
+      '@scope+react-start@1.0.0',
+      'node_modules',
+      '@scope',
+      'react-start',
+    )
+    writeJson(join(reactStartStore, 'package.json'), {
+      name: '@scope/react-start',
+      version: '1.0.0',
+      intent: { version: 1, repo: 'scope/react-start', docs: 'docs/' },
+      dependencies: { '@scope/start-core': '1.0.0' },
+    })
+    writeSkillMd(createDir(reactStartStore, 'skills', 'react-start'), {
+      name: 'react-start',
+      description: 'React start skill',
+      type: 'core',
+    })
+
+    // react-start's sibling link -> intermediate link -> real store dir.
+    createDir(pnpmDir, '@scope+react-start@1.0.0', 'node_modules', '@scope')
+    symlinkSync(
+      intermediateStartCore,
+      join(
+        pnpmDir,
+        '@scope+react-start@1.0.0',
+        'node_modules',
+        '@scope',
+        'start-core',
+      ),
+    )
+
+    createDir(root, 'node_modules', '@scope')
+    symlinkSync(
+      reactStartStore,
+      join(root, 'node_modules', '@scope', 'react-start'),
+    )
+
+    const result = scanForIntents(root)
+
+    const startCore = result.packages.find(
+      (p) => p.name === '@scope/start-core',
+    )
+    expect(startCore).toBeDefined()
+    expect(startCore!.skills.map((s) => s.name)).toContain('start-core')
+    expect(result.conflicts).toEqual([])
+  })
+
   it('discovers sub-skills', () => {
     const pkgDir = createDir(root, 'node_modules', '@tanstack', 'db')
     writeJson(join(pkgDir, 'package.json'), {