diff --git a/packages/pi-coding-agent/src/core/package-manager.ts b/packages/pi-coding-agent/src/core/package-manager.ts
index 44209e04f..0e06eaa5f 100644
--- a/packages/pi-coding-agent/src/core/package-manager.ts
+++ b/packages/pi-coding-agent/src/core/package-manager.ts
@@ -1665,9 +1665,17 @@ export class DefaultPackageManager implements PackageManager {
 			userOverrides.extensions,
 			globalBaseDir,
 		);
+		// Ecosystem skills (~/.agents/skills/) take priority over legacy config-dir skills.
+		// Skip legacy dir entirely when migration has completed (marker file present).
+		const legacySkillsMigrated =
+			resolve(userDirs.skills) !== resolve(userAgentsSkillsDir) &&
+			existsSync(join(userDirs.skills, ".migrated-to-agents"));
+		const legacyUserSkillEntries = legacySkillsMigrated
+			? []
+			: collectAutoSkillEntries(userDirs.skills);
 		addResources(
 			"skills",
-			[...collectAutoSkillEntries(userDirs.skills), ...collectAutoSkillEntries(userAgentsSkillsDir)],
+			[...collectAutoSkillEntries(userAgentsSkillsDir), ...legacyUserSkillEntries],
 			userMetadata,
 			userOverrides.skills,
 			globalBaseDir,
diff --git a/packages/pi-coding-agent/src/core/skills.ts b/packages/pi-coding-agent/src/core/skills.ts
index 9ab4df3b7..a8ab488ef 100644
--- a/packages/pi-coding-agent/src/core/skills.ts
+++ b/packages/pi-coding-agent/src/core/skills.ts
@@ -426,9 +426,9 @@ export function loadSkills(options: LoadSkillsOptions = {}): LoadSkillsResult {
 
 		// Legacy fallback: read skills from ~/.gsd/agent/skills/ so existing
 		// installs keep working until the one-time migration in resource-loader
-		// copies them to ~/.agents/skills/. Collision dedup above means already-
-		// migrated skills won't load twice.
-		if (LEGACY_SKILLS_DIR !== ECOSYSTEM_SKILLS_DIR && existsSync(LEGACY_SKILLS_DIR)) {
+		// copies them to ~/.agents/skills/. Skip if migration has completed.
+		const legacyMigrated = existsSync(join(LEGACY_SKILLS_DIR, ".migrated-to-agents"));
+		if (LEGACY_SKILLS_DIR !== ECOSYSTEM_SKILLS_DIR && existsSync(LEGACY_SKILLS_DIR) && !legacyMigrated) {
 			addSkills(loadSkillsFromDirInternal(LEGACY_SKILLS_DIR, "user", true));
 		}
 	}
diff --git a/src/resources/extensions/gsd/preferences-skills.ts b/src/resources/extensions/gsd/preferences-skills.ts
index 59bd4cf69..1ad5a6d39 100644
--- a/src/resources/extensions/gsd/preferences-skills.ts
+++ b/src/resources/extensions/gsd/preferences-skills.ts
@@ -32,9 +32,9 @@ export function getSkillSearchDirs(cwd: string): Array<{ dir: string; method: Sk
     { dir: join(homedir(), ".agents", "skills"), method: "user-skill" },
     { dir: join(cwd, ".agents", "skills"), method: "project-skill" },
   ];
-  // Legacy fallback — read skills from old GSD directory until migration completes
+  // Legacy fallback — read skills from old GSD directory only if migration hasn't completed
   const legacyDir = join(homedir(), ".gsd", "agent", "skills");
-  if (existsSync(legacyDir)) {
+  if (existsSync(legacyDir) && !existsSync(join(legacyDir, ".migrated-to-agents"))) {
     dirs.push({ dir: legacyDir, method: "user-skill" });
   }
   return dirs;
diff --git a/src/resources/extensions/gsd/skill-telemetry.ts b/src/resources/extensions/gsd/skill-telemetry.ts
index 33c427c4c..f1bddfd21 100644
--- a/src/resources/extensions/gsd/skill-telemetry.ts
+++ b/src/resources/extensions/gsd/skill-telemetry.ts
@@ -33,8 +33,9 @@ export function captureAvailableSkills(): void {
   const skillsDir = join(homedir(), ".agents", "skills");
   const legacyDir = join(homedir(), ".gsd", "agent", "skills");
   const names = listSkillNames(skillsDir);
-  // Include skills still in the legacy directory (pre-migration users)
-  const legacyNames = listSkillNames(legacyDir);
+  // Include skills still in the legacy directory only if migration hasn't completed
+  const legacyMigrated = existsSync(join(legacyDir, ".migrated-to-agents"));
+  const legacyNames = legacyMigrated ? [] : listSkillNames(legacyDir);
   const all = new Set([...names, ...legacyNames]);
   availableSkills = [...all];
   activelyLoadedSkills.clear();
@@ -106,7 +107,9 @@ export function detectStaleSkills(
   // Check all installed skills, not just those with usage data
   const skillsDir = join(homedir(), ".agents", "skills");
   const legacyDir = join(homedir(), ".gsd", "agent", "skills");
-  const installedSet = new Set([...listSkillNames(skillsDir), ...listSkillNames(legacyDir)]);
+  const legacyMigrated = existsSync(join(legacyDir, ".migrated-to-agents"));
+  const legacyNames = legacyMigrated ? [] : listSkillNames(legacyDir);
+  const installedSet = new Set([...listSkillNames(skillsDir), ...legacyNames]);
   const installed = [...installedSet];
 
   for (const skill of installed) {