diff --git a/src/parsers/claude.ts b/src/parsers/claude.ts
index 5262e91d56..52611abf02 100644
--- a/src/parsers/claude.ts
+++ b/src/parsers/claude.ts
@@ -193,7 +193,15 @@ function resolveComponentDirs(
   for (const entry of toPathList(custom)) {
     dirs.push(resolveWithinRoot(root, entry, `${defaultDir} path`))
   }
-  return dirs
+  // Deduplicate by resolved path so a manifest that declares the default
+  // directory explicitly (e.g. `"skills": "./skills/"`) does not scan it twice.
+  const seen = new Set<string>()
+  return dirs.filter((dir) => {
+    const resolved = path.resolve(dir)
+    if (seen.has(resolved)) return false
+    seen.add(resolved)
+    return true
+  })
 }
 
 function toPathList(value?: string | string[]): string[] {
diff --git a/tests/claude-parser.test.ts b/tests/claude-parser.test.ts
index 24f5b8fda3..4a0305e6d5 100644
--- a/tests/claude-parser.test.ts
+++ b/tests/claude-parser.test.ts
@@ -14,6 +14,7 @@ const fixtureNames = [
   "invalid-command-path",
   "invalid-hooks-path",
   "invalid-mcp-path",
+  "default-dir-declared",
 ] as const
 const fixtures = fixtureNames.map((name) =>
   materializeClaudePluginFixture(path.join(import.meta.dir, "fixtures", name)),
@@ -25,6 +26,7 @@ const [
   invalidCommandPathRoot,
   invalidHooksPathRoot,
   invalidMcpPathRoot,
+  defaultDirDeclaredRoot,
 ] = fixtures.map((fixture) => fixture.root)
 const tempRoots: string[] = []
 
@@ -190,6 +192,11 @@ describe("loadClaudePlugin", () => {
     expect(plugin.hooks?.hooks.PostToolUse?.[0]?.hooks[0]?.command).toBe("echo custom")
   })
 
+  test("does not double-count skills when the manifest declares the default dir", async () => {
+    const plugin = await loadClaudePlugin(defaultDirDeclaredRoot)
+    expect(plugin.skills.map((skill) => skill.name).sort()).toEqual(["skill-a", "skill-b"])
+  })
+
   test("rejects custom component paths that escape the plugin root", async () => {
     await expect(loadClaudePlugin(invalidCommandPathRoot)).rejects.toThrow(
       "Invalid commands path: ../outside-commands. Paths must stay within the plugin root.",
diff --git a/tests/fixtures/default-dir-declared/claude-plugin/plugin.json b/tests/fixtures/default-dir-declared/claude-plugin/plugin.json
new file mode 100644
index 0000000000..e5e04c84f6
--- /dev/null
+++ b/tests/fixtures/default-dir-declared/claude-plugin/plugin.json
@@ -0,0 +1,5 @@
+{
+  "name": "default-dir-declared",
+  "version": "1.0.0",
+  "skills": "./skills/"
+}
diff --git a/tests/fixtures/default-dir-declared/skills/skill-a/SKILL.md b/tests/fixtures/default-dir-declared/skills/skill-a/SKILL.md
new file mode 100644
index 0000000000..c6b1c5c893
--- /dev/null
+++ b/tests/fixtures/default-dir-declared/skills/skill-a/SKILL.md
@@ -0,0 +1,6 @@
+---
+name: skill-a
+description: Skill A
+---
+
+Skill A body.
diff --git a/tests/fixtures/default-dir-declared/skills/skill-b/SKILL.md b/tests/fixtures/default-dir-declared/skills/skill-b/SKILL.md
new file mode 100644
index 0000000000..ef1cb79c7a
--- /dev/null
+++ b/tests/fixtures/default-dir-declared/skills/skill-b/SKILL.md
@@ -0,0 +1,6 @@
+---
+name: skill-b
+description: Skill B
+---
+
+Skill B body.