diff --git a/src/haiku/rag/app.py b/src/haiku/rag/app.py
index b8e3c6d0..371b571f 100644
--- a/src/haiku/rag/app.py
+++ b/src/haiku/rag/app.py
@@ -5,6 +5,7 @@ from rich.console import Console
 from rich.markdown import Markdown
 
 from haiku.rag.client import HaikuRAG
+from haiku.rag.config import Config
 from haiku.rag.mcp import create_mcp_server
 from haiku.rag.monitor import FileWatcher
 from haiku.rag.store.models.chunk import Chunk
@@ -93,7 +94,7 @@ class HaikuRAGApp:
 
     async def serve(self, transport: str | None = None):
         """Start the MCP server."""
-        monitor = FileWatcher(paths=[])
+        monitor = FileWatcher(paths=Config.MONITOR_DIRECTORIES)
         asyncio.create_task(monitor.observe())
         server = create_mcp_server(self.db_path)
 
diff --git a/src/haiku/rag/config.py b/src/haiku/rag/config.py
index ffbe3054..6483a092 100644
--- a/src/haiku/rag/config.py
+++ b/src/haiku/rag/config.py
@@ -2,7 +2,7 @@ import os
 from pathlib import Path
 
 from dotenv import load_dotenv
-from pydantic import BaseModel
+from pydantic import BaseModel, field_validator
 
 from haiku.rag.utils import get_default_data_dir
 
@@ -13,6 +13,7 @@ class AppConfig(BaseModel):
     ENV: str = "development"
 
     DEFAULT_DATA_DIR: Path = get_default_data_dir()
+    MONITOR_DIRECTORIES: list[Path] = []
 
     EMBEDDING_PROVIDER: str = "ollama"
     EMBEDDING_MODEL: str = "mxbai-embed-large"
@@ -23,6 +24,17 @@ class AppConfig(BaseModel):
 
     OLLAMA_BASE_URL: str = "http://localhost:11434"
 
+    @field_validator("MONITOR_DIRECTORIES", mode="before")
+    @classmethod
+    def parse_monitor_directories(cls, v):
+        if isinstance(v, str):
+            if not v.strip():
+                return []
+            return [
+                Path(path.strip()).absolute() for path in v.split(",") if path.strip()
+            ]
+        return v
+
 
 # Expose Config object for app to import
 Config = AppConfig.model_validate(os.environ)
diff --git a/src/haiku/rag/monitor.py b/src/haiku/rag/monitor.py
index dccdb764..be12f9d9 100644
--- a/src/haiku/rag/monitor.py
+++ b/src/haiku/rag/monitor.py
@@ -10,7 +10,7 @@ logger = get_logger()
 
 
 class FileFilter(DefaultFilter):
-    def __init__(self, *, ignore_paths: list[str | Path] | None = None) -> None:
+    def __init__(self, *, ignore_paths: list[Path] | None = None) -> None:
         self.extensions = tuple(FileReader.extensions)
         super().__init__(ignore_paths=ignore_paths)
 
@@ -19,7 +19,7 @@ class FileFilter(DefaultFilter):
 
 
 class FileWatcher:
-    def __init__(self, paths: list[str | Path]):
+    def __init__(self, paths: list[Path]):
         self.paths = paths
 
     async def observe(self):
@@ -37,10 +37,8 @@ class FileWatcher:
             elif change == Change.deleted:
                 await self._delete_document(Path(path))
 
-    async def refresh(self, paths: list[str | Path] | None = None):
-        if paths is None:
-            paths = self.paths
-        for path in paths:
+    async def refresh(self):
+        for path in self.paths:
             for f in Path(path).rglob("**/*"):
                 if f.is_file() and f.suffix in FileReader.extensions:
                     await self._upsert_document(f)