diff --git a/agentex/src/config/mongodb_indexes.py b/agentex/src/config/mongodb_indexes.py
index d87231c3..d4458907 100644
--- a/agentex/src/config/mongodb_indexes.py
+++ b/agentex/src/config/mongodb_indexes.py
@@ -84,12 +84,34 @@ def ensure_mongodb_indexes(mongodb_database: MongoDBDatabase) -> None:
                     logger.info(f"  ✓ Created index '{name or result}'")
 
             except OperationFailure as e:
-                # Index might already exist with different options
+                # Index already exists with different options — drop and recreate
                 if "already exists with different options" in str(e):
+                    index_name = index_spec.get("name", "unnamed")
                     logger.warning(
-                        f"  ⚠ Index '{index_spec.get('name', 'unnamed')}' already exists "
-                        f"with different options. You may need to drop and recreate it."
+                        f"  ⚠ Index '{index_name}' already exists "
+                        f"with different options. Dropping and recreating..."
                     )
+                    try:
+                        collection.drop_index(index_name)
+                        logger.info(f"  ✓ Dropped existing index '{index_name}'")
+                    except Exception as drop_err:
+                        logger.error(
+                            f"  ✗ Failed to drop index '{index_name}': {drop_err}"
+                        )
+                        continue
+
+                    try:
+                        collection.create_index(keys, **index_kwargs)
+                        logger.info(f"  ✓ Recreated index '{index_name}'")
+                    except Exception as create_err:
+                        logger.error(
+                            f"  ✗ Failed to recreate index '{index_name}' after dropping it: {create_err}. "
+                            f"The index is currently absent. Restart the application or recreate it manually."
+                        )
+                        # Re-raise to abort startup. Note: this propagates past the
+                        # sibling `except Exception` below — Python only routes exceptions
+                        # from the `try` block to sibling handlers, not from other handlers.
+                        raise
                 else:
                     logger.error(f"  ✗ Failed to create index: {e}")
             except Exception as e:
@@ -97,6 +119,25 @@ def ensure_mongodb_indexes(mongodb_database: MongoDBDatabase) -> None:
                     f"  ✗ Unexpected error creating index '{index_spec.get('name', 'unnamed')}': {e}"
                 )
 
+    # Clean up legacy indexes that were removed from INDEXES lists but may
+    # still exist on databases where they were previously created.
+    legacy_indexes: list[tuple[str, str]] = [
+        ("messages", "task_id_idx"),
+        ("task_states", "task_id_idx"),
+    ]
+    for collection_name, index_name in legacy_indexes:
+        try:
+            mongodb_database[collection_name].drop_index(index_name)
+            logger.info(
+                f"  ✓ Dropped legacy index '{index_name}' from '{collection_name}'"
+            )
+        except OperationFailure:
+            pass  # Index doesn't exist — already clean
+        except Exception as e:
+            logger.warning(
+                f"  ⚠ Failed to drop legacy index '{index_name}' from '{collection_name}': {e}"
+            )
+
     logger.info("MongoDB index creation completed.")
 
 
diff --git a/agentex/src/domain/repositories/task_message_repository.py b/agentex/src/domain/repositories/task_message_repository.py
index 8d5e1e30..92ab9ac2 100644
--- a/agentex/src/domain/repositories/task_message_repository.py
+++ b/agentex/src/domain/repositories/task_message_repository.py
@@ -19,15 +19,13 @@ class TaskMessageRepository(MongoDBCRUDRepository[TaskMessageEntity]):
     # These will be created once at startup, not per request
     INDEXES = [
         {
-            "keys": [("task_id", pymongo.ASCENDING), ("created_at", pymongo.ASCENDING)],
+            "keys": [
+                ("task_id", pymongo.ASCENDING),
+                ("created_at", pymongo.DESCENDING),
+            ],
             "name": "task_id_created_at_idx",
             "description": "Compound index for querying messages by task_id and sorting by created_at",
         },
-        {
-            "keys": [("task_id", pymongo.ASCENDING)],
-            "name": "task_id_idx",
-            "description": "Single index for task_id queries and delete operations",
-        },
         {
             "keys": [
                 ("task_id", pymongo.ASCENDING),
@@ -40,7 +38,7 @@ class TaskMessageRepository(MongoDBCRUDRepository[TaskMessageEntity]):
             "keys": [
                 ("task_id", pymongo.ASCENDING),
                 ("content.type", pymongo.ASCENDING),
-                ("created_at", pymongo.ASCENDING),
+                ("created_at", pymongo.DESCENDING),
             ],
             "name": "task_id_content_type_created_at_idx",
             "description": "Compound index for filtering messages by task_id, content type, and sorting by created_at",
diff --git a/agentex/src/domain/repositories/task_state_repository.py b/agentex/src/domain/repositories/task_state_repository.py
index 16e43147..dddd10a1 100644
--- a/agentex/src/domain/repositories/task_state_repository.py
+++ b/agentex/src/domain/repositories/task_state_repository.py
@@ -1,3 +1,4 @@
+import asyncio
 from typing import Annotated
 
 import pymongo
@@ -21,12 +22,8 @@ class TaskStateRepository(MongoDBCRUDRepository[StateEntity]):
         {
             "keys": [("task_id", pymongo.ASCENDING), ("agent_id", pymongo.ASCENDING)],
             "name": "task_agent_compound_idx",
-            "description": "Compound index for get_by_task_and_agent queries",
-        },
-        {
-            "keys": [("task_id", pymongo.ASCENDING)],
-            "name": "task_id_idx",
-            "description": "Single index for task_id queries",
+            "unique": True,
+            "description": "Unique compound index for get_by_task_and_agent queries",
         },
         {
             "keys": [("agent_id", pymongo.ASCENDING)],
@@ -43,7 +40,13 @@ def __init__(self, db: DMongoDBDatabase):
     async def get_by_task_and_agent(
         self, task_id: str, agent_id: str
     ) -> StateEntity | None:
-        doc = self.collection.find_one({"task_id": task_id, "agent_id": agent_id})
+        loop = asyncio.get_running_loop()
+        doc = await loop.run_in_executor(
+            None,
+            lambda: self.collection.find_one(
+                {"task_id": task_id, "agent_id": agent_id}
+            ),
+        )
         return self._deserialize(doc) if doc else None