diff --git a/backend/packages/harness/deerflow/agents/lead_agent/prompt.py b/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
index e1eaf69..add4374 100644
--- a/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
+++ b/backend/packages/harness/deerflow/agents/lead_agent/prompt.py
@@ -1,8 +1,11 @@
+import logging
 from datetime import datetime
 
 from deerflow.config.agents_config import load_agent_soul
 from deerflow.skills import load_skills
 
+logger = logging.getLogger(__name__)
+
 
 def _build_subagent_section(max_concurrent: int) -> str:
     """Build the subagent system prompt section with dynamic concurrency limit.
@@ -364,7 +367,7 @@ def _get_memory_context(agent_name: str | None = None) -> str:
 </memory>
 """
     except Exception as e:
-        print(f"Failed to load memory context: {e}")
+        logger.error("Failed to load memory context: %s", e)
         return ""
 
 
diff --git a/backend/packages/harness/deerflow/agents/memory/queue.py b/backend/packages/harness/deerflow/agents/memory/queue.py
index 4184a52..a9a6838 100644
--- a/backend/packages/harness/deerflow/agents/memory/queue.py
+++ b/backend/packages/harness/deerflow/agents/memory/queue.py
@@ -1,5 +1,6 @@
 """Memory update queue with debounce mechanism."""
 
+import logging
 import threading
 import time
 from dataclasses import dataclass, field
@@ -8,6 +9,8 @@ from typing import Any
 
 from deerflow.config.memory_config import get_memory_config
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class ConversationContext:
@@ -61,7 +64,7 @@ class MemoryUpdateQueue:
             # Reset or start the debounce timer
             self._reset_timer()
 
-        print(f"Memory update queued for thread {thread_id}, queue size: {len(self._queue)}")
+        logger.info("Memory update queued for thread %s, queue size: %d", thread_id, len(self._queue))
 
     def _reset_timer(self) -> None:
         """Reset the debounce timer."""
@@ -79,7 +82,7 @@ class MemoryUpdateQueue:
         self._timer.daemon = True
         self._timer.start()
 
-        print(f"Memory update timer set for {config.debounce_seconds}s")
+        logger.debug("Memory update timer set for %ss", config.debounce_seconds)
 
     def _process_queue(self) -> None:
         """Process all queued conversation contexts."""
@@ -100,25 +103,25 @@ class MemoryUpdateQueue:
             self._queue.clear()
             self._timer = None
 
-        print(f"Processing {len(contexts_to_process)} queued memory updates")
+        logger.info("Processing %d queued memory updates", len(contexts_to_process))
 
         try:
             updater = MemoryUpdater()
 
             for context in contexts_to_process:
                 try:
-                    print(f"Updating memory for thread {context.thread_id}")
+                    logger.info("Updating memory for thread %s", context.thread_id)
                     success = updater.update_memory(
                         messages=context.messages,
                         thread_id=context.thread_id,
                         agent_name=context.agent_name,
                     )
                     if success:
-                        print(f"Memory updated successfully for thread {context.thread_id}")
+                        logger.info("Memory updated successfully for thread %s", context.thread_id)
                     else:
-                        print(f"Memory update skipped/failed for thread {context.thread_id}")
+                        logger.warning("Memory update skipped/failed for thread %s", context.thread_id)
                 except Exception as e:
-                    print(f"Error updating memory for thread {context.thread_id}: {e}")
+                    logger.error("Error updating memory for thread %s: %s", context.thread_id, e)
 
                 # Small delay between updates to avoid rate limiting
                 if len(contexts_to_process) > 1:
diff --git a/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py
index d29987d..5074d8d 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/clarification_middleware.py
@@ -1,5 +1,6 @@
 """Middleware for intercepting clarification requests and presenting them to the user."""
 
+import logging
 from collections.abc import Callable
 from typing import override
 
@@ -10,6 +11,8 @@ from langgraph.graph import END
 from langgraph.prebuilt.tool_node import ToolCallRequest
 from langgraph.types import Command
 
+logger = logging.getLogger(__name__)
+
 
 class ClarificationMiddlewareState(AgentState):
     """Compatible with the `ThreadState` schema."""
@@ -101,8 +104,8 @@ class ClarificationMiddleware(AgentMiddleware[ClarificationMiddlewareState]):
         args = request.tool_call.get("args", {})
         question = args.get("question", "")
 
-        print("[ClarificationMiddleware] Intercepted clarification request")
-        print(f"[ClarificationMiddleware] Question: {question}")
+        logger.info("Intercepted clarification request")
+        logger.debug("Clarification question: %s", question)
 
         # Format the clarification message
         formatted_message = self._format_clarification_message(args)
diff --git a/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py
index 7dc01d1..31d339f 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/memory_middleware.py
@@ -1,5 +1,6 @@
 """Middleware for memory mechanism."""
 
+import logging
 import re
 from typing import Any, override
 
@@ -10,6 +11,8 @@ from langgraph.runtime import Runtime
 from deerflow.agents.memory.queue import get_memory_queue
 from deerflow.config.memory_config import get_memory_config
 
+logger = logging.getLogger(__name__)
+
 
 class MemoryMiddlewareState(AgentState):
     """Compatible with the `ThreadState` schema."""
@@ -122,13 +125,13 @@ class MemoryMiddleware(AgentMiddleware[MemoryMiddlewareState]):
         # Get thread ID from runtime context
         thread_id = runtime.context.get("thread_id") if runtime.context else None
         if not thread_id:
-            print("MemoryMiddleware: No thread_id in context, skipping memory update")
+            logger.debug("No thread_id in context, skipping memory update")
             return None
 
         # Get messages from state
         messages = state.get("messages", [])
         if not messages:
-            print("MemoryMiddleware: No messages in state, skipping memory update")
+            logger.debug("No messages in state, skipping memory update")
             return None
 
         # Filter to only keep user inputs and final assistant responses
diff --git a/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py
index 948085b..c25531e 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/thread_data_middleware.py
@@ -1,3 +1,4 @@
+import logging
 from typing import NotRequired, override
 
 from langchain.agents import AgentState
@@ -8,6 +9,8 @@ from langgraph.runtime import Runtime
 from deerflow.agents.thread_state import ThreadDataState
 from deerflow.config.paths import Paths, get_paths
 
+logger = logging.getLogger(__name__)
+
 
 class ThreadDataMiddlewareState(AgentState):
     """Compatible with the `ThreadState` schema."""
@@ -87,7 +90,7 @@ class ThreadDataMiddleware(AgentMiddleware[ThreadDataMiddlewareState]):
         else:
             # Eager initialization: create directories immediately
             paths = self._create_thread_directories(thread_id)
-            print(f"Created thread data directories for thread {thread_id}")
+            logger.debug("Created thread data directories for thread %s", thread_id)
 
         return {
             "thread_data": {
diff --git a/backend/packages/harness/deerflow/agents/middlewares/view_image_middleware.py b/backend/packages/harness/deerflow/agents/middlewares/view_image_middleware.py
index 29b3871..2870624 100644
--- a/backend/packages/harness/deerflow/agents/middlewares/view_image_middleware.py
+++ b/backend/packages/harness/deerflow/agents/middlewares/view_image_middleware.py
@@ -1,5 +1,6 @@
 """Middleware for injecting image details into conversation before LLM call."""
 
+import logging
 from typing import NotRequired, override
 
 from langchain.agents import AgentState
@@ -9,6 +10,8 @@ from langgraph.runtime import Runtime
 
 from deerflow.agents.thread_state import ViewedImageData
 
+logger = logging.getLogger(__name__)
+
 
 class ViewImageMiddlewareState(AgentState):
     """Compatible with the `ThreadState` schema."""
@@ -182,7 +185,7 @@ class ViewImageMiddleware(AgentMiddleware[ViewImageMiddlewareState]):
         # Create a new human message with mixed content (text + images)
         human_msg = HumanMessage(content=image_content)
 
-        print("[ViewImageMiddleware] Injecting image details message with images before LLM call")
+        logger.debug("Injecting image details message with images before LLM call")
 
         # Return state update with the new message
         return {"messages": [human_msg]}
diff --git a/backend/packages/harness/deerflow/skills/loader.py b/backend/packages/harness/deerflow/skills/loader.py
index 50c68d3..b596d62 100644
--- a/backend/packages/harness/deerflow/skills/loader.py
+++ b/backend/packages/harness/deerflow/skills/loader.py
@@ -1,9 +1,12 @@
+import logging
 import os
 from pathlib import Path
 
 from .parser import parse_skill_file
 from .types import Skill
 
+logger = logging.getLogger(__name__)
+
 
 def get_skills_root_path() -> Path:
     """
@@ -86,7 +89,7 @@ def load_skills(skills_path: Path | None = None, use_config: bool = True, enable
             skill.enabled = extensions_config.is_skill_enabled(skill.name, skill.category)
     except Exception as e:
         # If config loading fails, default to all enabled
-        print(f"Warning: Failed to load extensions config: {e}")
+        logger.warning("Failed to load extensions config: %s", e)
 
     # Filter by enabled status if requested
     if enabled_only:
diff --git a/backend/packages/harness/deerflow/skills/parser.py b/backend/packages/harness/deerflow/skills/parser.py
index fe1c04c..b7cb897 100644
--- a/backend/packages/harness/deerflow/skills/parser.py
+++ b/backend/packages/harness/deerflow/skills/parser.py
@@ -1,8 +1,11 @@
+import logging
 import re
 from pathlib import Path
 
 from .types import Skill
 
+logger = logging.getLogger(__name__)
+
 
 def parse_skill_file(skill_file: Path, category: str, relative_path: Path | None = None) -> Skill | None:
     """
@@ -61,5 +64,5 @@ def parse_skill_file(skill_file: Path, category: str, relative_path: Path | None
         )
 
     except Exception as e:
-        print(f"Error parsing skill file {skill_file}: {e}")
+        logger.error("Error parsing skill file %s: %s", skill_file, e)
         return None