diff --git a/packages/api/src/skills/sync/github.spec.ts b/packages/api/src/skills/sync/github.spec.ts
index cd36c2bc9e..ff5d47f190 100644
--- a/packages/api/src/skills/sync/github.spec.ts
+++ b/packages/api/src/skills/sync/github.spec.ts
@@ -463,6 +463,11 @@ describe('createGitHubSkillSyncRunner', () => {
 
     expect(result.status).toBe('completed');
     expect(observedTenantId).toBe('tenant-a');
+    expect(deps.findSkillBySourceIdentity).toHaveBeenCalledWith({
+      source: 'github',
+      upstreamId: 'librechat-skills:skills/research',
+      tenantId: 'tenant-a',
+    });
     expect(deps.createSkill).toHaveBeenCalledWith(
       expect.objectContaining({ name: 'research', tenantId: 'tenant-a' }),
     );
@@ -778,6 +783,7 @@ describe('createGitHubSkillSyncRunner', () => {
     expect(deps.findSkillBySourceIdentity).toHaveBeenCalledWith({
       source: 'github',
       upstreamId: 'librechat-skills:skills/research',
+      tenantId: undefined,
     });
     expect(deps.createSkill).not.toHaveBeenCalled();
     expect(deps.updateSkill).toHaveBeenCalledWith(
diff --git a/packages/api/src/skills/sync/github.ts b/packages/api/src/skills/sync/github.ts
index 1eda2f8009..1e326ad123 100644
--- a/packages/api/src/skills/sync/github.ts
+++ b/packages/api/src/skills/sync/github.ts
@@ -157,6 +157,7 @@ export type GitHubSkillSyncDeps = {
   findSkillBySourceIdentity: (params: {
     source: 'github' | 'notion';
     upstreamId: string;
+    tenantId?: string;
   }) => Promise<(ISkill & { _id: Types.ObjectId }) | null>;
   listSkillsBySource: (params: {
     source: 'github' | 'notion';
@@ -803,8 +804,12 @@ async function prepareRemoteSkill(params: {
     source: PROVIDER,
     sourceMetadata,
   };
-  const foundExisting = await deps.findSkillBySourceIdentity({ source: PROVIDER, upstreamId });
   const sourceTenantId = source.tenantId ?? undefined;
+  const foundExisting = await deps.findSkillBySourceIdentity({
+    source: PROVIDER,
+    upstreamId,
+    tenantId: sourceTenantId,
+  });
   const existing =
     foundExisting && (foundExisting.tenantId ?? undefined) === sourceTenantId
       ? foundExisting
diff --git a/packages/data-schemas/src/methods/skill.spec.ts b/packages/data-schemas/src/methods/skill.spec.ts
index 85ecf41bf8..fda6b045b1 100644
--- a/packages/data-schemas/src/methods/skill.spec.ts
+++ b/packages/data-schemas/src/methods/skill.spec.ts
@@ -507,6 +507,48 @@ describe('Skill CRUD methods', () => {
     expect(await SkillFile.countDocuments({ skillId: skill._id })).toBe(0);
   });
 
+  it('findSkillBySourceIdentity searches only the requested tenant bucket', async () => {
+    const upstreamId = 'librechat-skills:skills/research';
+    const sourceMetadata = {
+      provider: 'github',
+      sourceId: 'librechat-skills',
+      upstreamId,
+    };
+    const author = new mongoose.Types.ObjectId();
+    const tenantSkill = await Skill.create({
+      name: 'research',
+      description: 'A tenant-scoped GitHub skill mirror.',
+      body: 'tenant body',
+      author,
+      authorName: 'GitHub Sync',
+      tenantId: 'tenant-a',
+      source: 'github',
+      sourceMetadata,
+    });
+    const ambientSkill = await Skill.create({
+      name: 'research',
+      description: 'An ambient GitHub skill mirror.',
+      body: 'ambient body',
+      author,
+      authorName: 'GitHub Sync',
+      source: 'github',
+      sourceMetadata,
+    });
+
+    const ambientResult = await methods.findSkillBySourceIdentity({
+      source: 'github',
+      upstreamId,
+    });
+    const tenantResult = await methods.findSkillBySourceIdentity({
+      source: 'github',
+      upstreamId,
+      tenantId: 'tenant-a',
+    });
+
+    expect(ambientResult?._id.toString()).toBe(ambientSkill._id.toString());
+    expect(tenantResult?._id.toString()).toBe(tenantSkill._id.toString());
+  });
+
   it('listSkillsByAccess returns only accessible skills and paginates by cursor', async () => {
     const ids: mongoose.Types.ObjectId[] = [];
     for (let i = 0; i < 3; i++) {
diff --git a/packages/data-schemas/src/methods/skill.ts b/packages/data-schemas/src/methods/skill.ts
index 998ad9e8b5..64c9fad424 100644
--- a/packages/data-schemas/src/methods/skill.ts
+++ b/packages/data-schemas/src/methods/skill.ts
@@ -1365,11 +1365,16 @@ export function createSkillMethods(mongoose: typeof import('mongoose'), deps: Sk
   async function findSkillBySourceIdentity(params: {
     source: 'github' | 'notion';
     upstreamId: string;
+    tenantId?: string;
   }): Promise<(ISkill & { _id: Types.ObjectId }) | null> {
     const Skill = mongoose.models.Skill as Model<ISkillDocument>;
+    const tenantFilter: FilterQuery<ISkillDocument> = params.tenantId
+      ? { tenantId: params.tenantId }
+      : { $or: [{ tenantId: { $exists: false } }, { tenantId: null }] };
     const doc = await Skill.findOne({
       source: params.source,
       'sourceMetadata.upstreamId': params.upstreamId,
+      ...tenantFilter,
     }).lean();
     return (doc as unknown as (ISkill & { _id: Types.ObjectId }) | null) ?? null;
   }