diff --git a/scripts/python/modules.py b/scripts/python/modules.py
index fda61c5..b7158a6 100755
--- a/scripts/python/modules.py
+++ b/scripts/python/modules.py
@@ -371,12 +371,7 @@ def build_state(env_path: Path, manifest_path: Path) -> ModuleCollectionState:
     for unknown_key in extra_env_modules:
         warnings.append(f".env defines {unknown_key} but it is missing from the manifest")
 
-    # Warn if manifest entry lacks .env toggle (skip blocked modules)
-    for module in modules:
-        if not module.blocked and module.key not in env_map and module.key not in os.environ:
-            warnings.append(
-                f"Manifest includes {module.key} but .env does not define it (defaulting to 0)"
-            )
+    # Skip warnings for missing modules - they default to disabled (0) as intended
 
     return ModuleCollectionState(
         manifest_path=manifest_path,
diff --git a/setup.sh b/setup.sh
index 698be56..034e5e3 100755
--- a/setup.sh
+++ b/setup.sh
@@ -1724,7 +1724,11 @@ EOF
     echo
   echo "# Modules"
   for module_key in "${MODULE_KEYS[@]}"; do
-    printf "%s=%s\n" "$module_key" "${!module_key:-0}"
+    local module_value="${!module_key:-0}"
+    # Only write enabled modules (value=1) to .env
+    if [ "$module_value" = "1" ]; then
+      printf "%s=%s\n" "$module_key" "$module_value"
+    fi
   done
   cat <<EOF
 MODULES_REBUILD_SOURCE_PATH=$MODULES_REBUILD_SOURCE_PATH