diff --git a/glotaran/project/result.py b/glotaran/project/result.py
index fda9033e8..20f5564a4 100644
--- a/glotaran/project/result.py
+++ b/glotaran/project/result.py
@@ -39,11 +39,20 @@ class Config:
     parameters_intitial: Parameters
     parameters_optimized: Parameters
 
-    def save(self, path: Path, options: SavingOptions = SAVING_OPTIONS_DEFAULT):
+    def save(
+        self,
+        path: Path,
+        options: SavingOptions = SAVING_OPTIONS_DEFAULT,
+        allow_overwrite: bool = False,
+    ):
         if path.exists() and path.is_file():
-            raise GlotaranUserError("Save folder must be a path.")
-        path.mkdir()
+            raise GlotaranUserError("Save path must be a folder.")
+        if path.exists() and not allow_overwrite:
+            raise GlotaranUserError(
+                "Save path already exists. Use allow_overwrite=True to overwrite."
+            )
         result_dict: dict[str, Any] = {"data": {}, "experiments": {}}
+        path.mkdir(exist_ok=True, parents=True)
 
         # TODO: Save scheme or experiments
         #  experiment_folder = path / "experiments"
@@ -54,13 +63,13 @@ def save(self, path: Path, options: SavingOptions = SAVING_OPTIONS_DEFAULT):
         #      write_dict(experiment.dict(), experiment_path)
 
         data_path = path / "data"
-        data_path.mkdir()
+        data_path.mkdir(exist_ok=True)
         for label, data in self.data.items():
             dataset_path = data_path / f"{label}.{options.data_format}"
             result_dict["data"][label] = str(dataset_path)
             if options.data_filter is not None:
                 data = data[options.data_filter]
-            save_dataset(data, dataset_path)
+            save_dataset(data, dataset_path, allow_overwrite=allow_overwrite)
 
         optimization_history_path = path / "optimization_history.csv"
         result_dict["optimization_history"] = str(optimization_history_path)
@@ -68,11 +77,15 @@ def save(self, path: Path, options: SavingOptions = SAVING_OPTIONS_DEFAULT):
 
         parameters_initial_path = path / f"parameters_initial.{options.parameter_format}"
         result_dict["parameters_initial"] = str(parameters_initial_path)
-        save_parameters(self.parameters_intitial, parameters_initial_path)
+        save_parameters(
+            self.parameters_intitial, parameters_initial_path, allow_overwrite=allow_overwrite
+        )
 
         parameters_optimized_path = path / f"parameters_optimized.{options.parameter_format}"
         result_dict["parameters_optimized"] = str(parameters_optimized_path)
-        save_parameters(self.parameters_optimized, parameters_optimized_path)
+        save_parameters(
+            self.parameters_optimized, parameters_optimized_path, allow_overwrite=allow_overwrite
+        )
 
         result_path = path / "glotaran_result.yml"
         write_dict(result_dict, result_path)