diff --git a/.gitignore b/.gitignore
index 4e46d2e71..0076848e0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,6 +40,7 @@ coverage/
 skills/custom/*
 logs/
 log/
+debug.log
 
 # Local git hooks (keep only on this machine, do not push)
 .githooks/
diff --git a/backend/debug.py b/backend/debug.py
index 2031557c1..3e0694cef 100644
--- a/backend/debug.py
+++ b/backend/debug.py
@@ -19,10 +19,6 @@ import asyncio
 import logging
 
 from dotenv import load_dotenv
-from langchain_core.messages import HumanMessage
-from langgraph.runtime import Runtime
-
-from deerflow.agents import make_lead_agent
 
 try:
     from prompt_toolkit import PromptSession
@@ -34,18 +30,67 @@ except ImportError:
 
 load_dotenv()
 
-logging.basicConfig(
-    level=logging.INFO,
-    format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
-    datefmt="%Y-%m-%d %H:%M:%S",
-)
+_LOG_FMT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+_LOG_DATEFMT = "%Y-%m-%d %H:%M:%S"
+
+
+def _logging_level_from_config(name: str) -> int:
+    """Map ``config.yaml`` ``log_level`` string to a ``logging`` level constant."""
+    mapping = logging.getLevelNamesMapping()
+    return mapping.get((name or "info").strip().upper(), logging.INFO)
+
+
+def _setup_logging(log_level: str) -> None:
+    """Send application logs to ``debug.log`` at *log_level*; do not print them on the console.
+
+    Idempotent: any pre-existing handlers on the root logger (e.g. installed by
+    ``logging.basicConfig`` in transitively imported modules) are removed so the
+    debug session output only lands in ``debug.log``.
+    """
+    level = _logging_level_from_config(log_level)
+    root = logging.root
+    for h in list(root.handlers):
+        root.removeHandler(h)
+        h.close()
+    root.setLevel(level)
+
+    file_handler = logging.FileHandler("debug.log", mode="a", encoding="utf-8")
+    file_handler.setLevel(level)
+    file_handler.setFormatter(logging.Formatter(_LOG_FMT, datefmt=_LOG_DATEFMT))
+    root.addHandler(file_handler)
+
+
+def _update_logging_level(log_level: str) -> None:
+    """Update the root logger and existing handlers to *log_level*."""
+    level = _logging_level_from_config(log_level)
+    root = logging.root
+    root.setLevel(level)
+    for handler in root.handlers:
+        handler.setLevel(level)
 
 
 async def main():
+    # Install file logging first so warnings emitted while loading config do not
+    # leak onto the interactive terminal via Python's lastResort handler.
+    _setup_logging("info")
+
+    from deerflow.config import get_app_config
+
+    app_config = get_app_config()
+    _update_logging_level(app_config.log_level)
+
+    # Delay the rest of the deerflow imports until *after* logging is installed
+    # so that any import-time side effects (e.g. deerflow.agents starts a
+    # background skill-loader thread on import) emit logs to debug.log instead
+    # of leaking onto the interactive terminal via Python's lastResort handler.
+    from langchain_core.messages import HumanMessage
+    from langgraph.runtime import Runtime
+
+    from deerflow.agents import make_lead_agent
+    from deerflow.mcp import initialize_mcp_tools
+
     # Initialize MCP tools at startup
     try:
-        from deerflow.mcp import initialize_mcp_tools
-
         await initialize_mcp_tools()
     except Exception as e:
         print(f"Warning: Failed to initialize MCP tools: {e}")
@@ -71,6 +116,7 @@ async def main():
     print("=" * 50)
     print("Lead Agent Debug Mode")
     print("Type 'quit' or 'exit' to stop")
+    print(f"Logs: debug.log (log_level={app_config.log_level})")
     if not _HAS_PROMPT_TOOLKIT:
         print("Tip: `uv sync --group dev` to enable arrow-key & history support")
     print("=" * 50)