diff --git a/src/serena/agent.py b/src/serena/agent.py
index 59b98f1..4c50174 100644
--- a/src/serena/agent.py
+++ b/src/serena/agent.py
@@ -327,10 +327,19 @@ class SerenaConfig(SerenaConfigBase):
         num_project_migrations = 0
         for path in loaded_commented_yaml["projects"]:
             path = Path(path).resolve()
-            if not path.exists() or (path.is_dir() and not (path / ProjectConfig.rel_path_to_project_yml()).exists()):
-                log.warning(f"Project path {path} does not exist or does not contain a project configuration file, skipping.")
+            if not path.exists():
+                log.warning(f"Project path {path} does not exist, skipping.")
                 continue
+            if path.is_dir():
+                project_yml_path = path / ProjectConfig.rel_path_to_project_yml()
+                if not project_yml_path.exists():
+                    log.info(f"Project path {path} does not contain a project configuration file, creating one.")
+                    ProjectConfig.autogenerate(path, save_to_disk=True)
+                    continue
             if path.is_file():
+                log.info(
+                    f"Project path {path} is a file, migrating to in-project configuration. This is a legacy feature for backwards compatibility."
+                )
                 path = cls._migrate_out_of_project_config_file(path)
                 if path is None:
                     continue
diff --git a/src/serena/util/general.py b/src/serena/util/general.py
index bfddaf4..b350ae1 100644
--- a/src/serena/util/general.py
+++ b/src/serena/util/general.py
@@ -1,3 +1,4 @@
+import os
 from typing import Literal, overload
 
 from ruamel.yaml import YAML
@@ -26,5 +27,6 @@ def load_yaml(path: str, preserve_comments: bool = False) -> dict | CommentedMap
 
 def save_yaml(path: str, data: dict | CommentedMap, preserve_comments: bool = False) -> None:
     yaml = _create_YAML(preserve_comments)
+    os.makedirs(os.path.dirname(path), exist_ok=True)
     with open(path, "w", encoding="utf-8") as f:
         yaml.dump(data, f)