diff --git a/docs/configuration.md b/docs/configuration.md
index 4cb9973c..30d5b5f5 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -465,3 +465,13 @@ haiku-rag init-config --from-env
 ```
 
 This will read your current environment variables and generate a `haiku.rag.yaml` file with those settings.
+
+!!! note
+    When migrating from environment variables, list values like `MONITOR_DIRECTORIES` that were comma-separated (`/path1,/path2`) will be converted to proper YAML lists. In YAML, always use list syntax:
+
+    ```yaml
+    storage:
+      monitor_directories:
+        - /path/to/dir1
+        - /path/to/dir2
+    ```
diff --git a/src/haiku/rag/config/loader.py b/src/haiku/rag/config/loader.py
index c2bf1240..33d3dcd4 100644
--- a/src/haiku/rag/config/loader.py
+++ b/src/haiku/rag/config/loader.py
@@ -131,6 +131,13 @@ def load_config_from_env() -> dict:
     for env_var, path in env_mappings.items():
         value = os.getenv(env_var)
         if value is not None:
+            # Special handling for MONITOR_DIRECTORIES - parse comma-separated list
+            if env_var == "MONITOR_DIRECTORIES":
+                if value.strip():
+                    value = [p.strip() for p in value.split(",") if p.strip()]
+                else:
+                    value = []
+
             if isinstance(path, tuple):
                 current = result
                 for key in path[:-1]:
diff --git a/src/haiku/rag/config/models.py b/src/haiku/rag/config/models.py
index 3fdd6bc8..3bcc59d1 100644
--- a/src/haiku/rag/config/models.py
+++ b/src/haiku/rag/config/models.py
@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from pydantic import BaseModel, Field, field_validator
+from pydantic import BaseModel, Field
 
 from haiku.rag.utils import get_default_data_dir
 
@@ -76,20 +76,3 @@ class AppConfig(BaseModel):
     processing: ProcessingConfig = Field(default_factory=ProcessingConfig)
     providers: ProvidersConfig = Field(default_factory=ProvidersConfig)
     a2a: A2AConfig = Field(default_factory=A2AConfig)
-
-    @field_validator("storage", mode="before")
-    @classmethod
-    def parse_storage(cls, v):
-        """Parse storage config, handling comma-separated monitor directories."""
-        if isinstance(v, dict) and "monitor_directories" in v:
-            dirs = v["monitor_directories"]
-            if isinstance(dirs, str):
-                if not dirs.strip():
-                    v["monitor_directories"] = []
-                else:
-                    v["monitor_directories"] = [
-                        Path(path.strip()).absolute()
-                        for path in dirs.split(",")
-                        if path.strip()
-                    ]
-        return v