diff --git a/app/routers/documents.py b/app/routers/documents.py
index 4f4631d..d0d438c 100644
--- a/app/routers/documents.py
+++ b/app/routers/documents.py
@@ -230,21 +230,20 @@ async def list_documents(
 ):
     agent, api_role = await get_current_agent_or_api_token(request, db)
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=404, detail="Project not found")
-    else:
-        # API tokens don't have project-level access control here
-        # Access is controlled at document level via agent_type
-        pass
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=404, detail="Project not found")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     result = await db.execute(
         select(Document).where(
@@ -283,17 +282,20 @@ async def create_document(
 ):
     agent, api_role = await get_current_agent_or_api_token(request, db)
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=404, detail="Project not found")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=404, detail="Project not found")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     # Determine agent_type for the document
     doc_agent_type = payload.agent_type or "general"
@@ -353,21 +355,24 @@ async def get_document(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=404, detail="Document not found")
-    else:
-        # API tokens check role-based access
-        if not _can_access_document(api_role, doc.agent_type, require_write=False):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=404, detail="Document not found")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=False):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     return await document_to_response(db, doc)
 
@@ -391,21 +396,24 @@ async def update_document(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based write access
-        if not _can_access_document(api_role, doc.agent_type, require_write=True):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based write access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=True):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     if payload.title is not None:
         doc.title = payload.title
@@ -449,21 +457,24 @@ async def delete_document(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based write access
-        if not _can_access_document(api_role, doc.agent_type, require_write=True):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based write access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=True):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     doc.is_deleted = True
     doc.deleted_at = datetime.utcnow()
@@ -496,21 +507,24 @@ async def update_document_content(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based write access
-        if not _can_access_document(api_role, doc.agent_type, require_write=True):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based write access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=True):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     # Determine actual format based on content type (backward compatibility)
     # If content is a string, treat as markdown regardless of format field
@@ -566,21 +580,24 @@ async def restore_document(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based write access
-        if not _can_access_document(api_role, doc.agent_type, require_write=True):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based write access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=True):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     doc.is_deleted = False
     doc.deleted_at = None
@@ -608,21 +625,24 @@ async def assign_tags(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based write access
-        if not _can_access_document(api_role, doc.agent_type, require_write=True):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based write access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=True):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     for tag_id in payload.tag_ids:
         tag_result = await db.execute(
@@ -668,21 +688,24 @@ async def remove_tag(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
 
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based write access
-        if not _can_access_document(api_role, doc.agent_type, require_write=True):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # Check role-based write access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=True):
+        raise HTTPException(status_code=403, detail="Forbidden")
 
     await db.execute(
         delete(DocumentTag).where(
@@ -717,21 +740,24 @@ async def _get_doc_with_access(
     if not doc:
         raise HTTPException(status_code=404, detail="Document not found")
     
-    # JWT tokens check project ownership
-    if api_role is None:
-        proj_result = await db.execute(
-            select(Project).where(
-                Project.id == doc.project_id,
-                Project.agent_id == agent.id,
-                Project.is_deleted == False,
-            )
+    # Check project ownership
+    proj_result = await db.execute(
+        select(Project).where(
+            Project.id == doc.project_id,
+            Project.is_deleted == False,
         )
-        if not proj_result.scalar_one_or_none():
-            raise HTTPException(status_code=403, detail="Forbidden")
-    else:
-        # API tokens check role-based access
-        if not _can_access_document(api_role, doc.agent_type, require_write=require_write):
-            raise HTTPException(status_code=403, detail="Forbidden")
+    )
+    project = proj_result.scalar_one_or_none()
+    if not project:
+        raise HTTPException(status_code=403, detail="Forbidden")
+
+    # For API tokens, verify project belongs to the token owner
+    if api_role is not None and project.agent_id != agent.id:
+        raise HTTPException(status_code=403, detail="Forbidden")
+    
+    # Check role-based access for API tokens
+    if api_role is not None and not _can_access_document(api_role, doc.agent_type, require_write=require_write):
+        raise HTTPException(status_code=403, detail="Forbidden")
     
     return doc, api_role
 
diff --git a/tests/test_api_tokens.py b/tests/test_api_tokens.py
index 622d57f..662f881 100644
--- a/tests/test_api_tokens.py
+++ b/tests/test_api_tokens.py
@@ -257,3 +257,88 @@ async def test_api_token_auth_flow(client, admin_user):
         headers={"Authorization": f"Bearer {researcher_token}"}
     )
     assert get_resp.status_code == 403
+
+
+@pytest.mark.asyncio
+async def test_api_token_cannot_access_other_user_project(client, admin_user):
+    """Test that API token can only access projects belonging to the token owner."""
+    # Create another user
+    import uuid
+    import bcrypt
+    from sqlalchemy import text
+    
+    password_hash = bcrypt.hashpw("user2pass".encode(), bcrypt.gensalt()).decode()
+    
+    async with async_engine.begin() as conn:
+        user2_id = str(uuid.uuid4())
+        await conn.execute(
+            text("""
+                INSERT INTO agents (id, username, password_hash, role, is_deleted, created_at, updated_at)
+                VALUES (:id, :username, :password_hash, 'agent', 0, datetime('now'), datetime('now'))
+            """),
+            {
+                "id": user2_id,
+                "username": "user2",
+                "password_hash": password_hash
+            }
+        )
+    
+    # Login as user2
+    login_resp = await client.post(
+        "/api/v1/auth/login",
+        json={"username": "user2", "password": "user2pass"}
+    )
+    user2_token = login_resp.json()["access_token"]
+    
+    # Create project by user2
+    proj_resp = await client.post(
+        "/api/v1/projects",
+        json={"name": "User2 Project"},
+        headers={"Authorization": f"Bearer {user2_token}"}
+    )
+    user2_proj_id = proj_resp.json()["id"]
+    
+    # Create document in user2's project
+    doc_resp = await client.post(
+        f"/api/v1/projects/{user2_proj_id}/documents",
+        json={"title": "User2 Doc", "content": "Content", "agent_type": "general"},
+        headers={"Authorization": f"Bearer {user2_token}"}
+    )
+    user2_doc_id = doc_resp.json()["id"]
+    
+    # Admin creates a researcher token
+    gen_resp = await client.post(
+        "/api/v1/auth/token/generate",
+        json={"name": "research-token", "role": "researcher"},
+        headers={"Authorization": f"Bearer {admin_user}"}
+    )
+    researcher_token = gen_resp.json()["token"]
+    
+    # Admin creates a project and document
+    admin_proj_resp = await client.post(
+        "/api/v1/projects",
+        json={"name": "Admin Project"},
+        headers={"Authorization": f"Bearer {admin_user}"}
+    )
+    admin_proj_id = admin_proj_resp.json()["id"]
+    
+    admin_doc_resp = await client.post(
+        f"/api/v1/projects/{admin_proj_id}/documents",
+        json={"title": "Admin Doc", "content": "Content", "agent_type": "research"},
+        headers={"Authorization": f"Bearer {admin_user}"}
+    )
+    admin_doc_id = admin_doc_resp.json()["id"]
+    
+    # Researcher token should NOT be able to access user2's project/document
+    get_resp = await client.get(
+        f"/api/v1/documents/{user2_doc_id}",
+        headers={"Authorization": f"Bearer {researcher_token}"}
+    )
+    assert get_resp.status_code == 403
+    
+    # Researcher token SHOULD be able to access admin's research document
+    get_resp = await client.get(
+        f"/api/v1/documents/{admin_doc_id}",
+        headers={"Authorization": f"Bearer {researcher_token}"}
+    )
+    assert get_resp.status_code == 200