diff --git a/monai/apps/auto3dseg/auto_runner.py b/monai/apps/auto3dseg/auto_runner.py
index 23fb3eb250..80ae34180e 100644
--- a/monai/apps/auto3dseg/auto_runner.py
+++ b/monai/apps/auto3dseg/auto_runner.py
@@ -83,6 +83,8 @@ class AutoRunner:
             zip url will be downloaded and extracted into the work_dir.
         allow_skip: a switch passed to BundleGen process which determines if some Algo in the default templates
             can be skipped based on the analysis on the dataset from Auto3DSeg DataAnalyzer.
+        mlflow_tracking_uri: a tracking URI for MLflow server which could be local directory or address of the remote
+            tracking Server; MLflow runs will be recorded locally in algorithms' model folder if the value is None.
         kwargs: image writing parameters for the ensemble inference. The kwargs format follows the SaveImage
             transform. For more information, check https://docs.monai.io/en/stable/transforms.html#saveimage.
 
@@ -209,6 +211,7 @@ def __init__(
         not_use_cache: bool = False,
         templates_path_or_url: str | None = None,
         allow_skip: bool = True,
+        mlflow_tracking_uri: str | None = None,
         **kwargs: Any,
     ):
         logger.info(f"AutoRunner using work directory {work_dir}")
@@ -220,6 +223,7 @@ def __init__(
         self.algos = algos
         self.templates_path_or_url = templates_path_or_url
         self.allow_skip = allow_skip
+        self.mlflow_tracking_uri = mlflow_tracking_uri
         self.kwargs = deepcopy(kwargs)
 
         if input is None and os.path.isfile(self.data_src_cfg_name):
@@ -783,6 +787,7 @@ def run(self):
                 templates_path_or_url=self.templates_path_or_url,
                 data_stats_filename=self.datastats_filename,
                 data_src_cfg_name=self.data_src_cfg_name,
+                mlflow_tracking_uri=self.mlflow_tracking_uri,
             )
 
             if self.gpu_customization:
diff --git a/monai/apps/auto3dseg/bundle_gen.py b/monai/apps/auto3dseg/bundle_gen.py
index a091739dd3..03b9c8bbf4 100644
--- a/monai/apps/auto3dseg/bundle_gen.py
+++ b/monai/apps/auto3dseg/bundle_gen.py
@@ -85,6 +85,7 @@ def __init__(self, template_path: PathLike):
         self.template_path = template_path
         self.data_stats_files = ""
         self.data_list_file = ""
+        self.mlflow_tracking_uri = None
         self.output_path = ""
         self.name = ""
         self.best_metric = None
@@ -129,6 +130,17 @@ def set_data_source(self, data_src_cfg: str) -> None:
         """
         self.data_list_file = data_src_cfg
 
+    def set_mlflow_tracking_uri(self, mlflow_tracking_uri: str | None) -> None:
+        """
+        Set the tracking URI for MLflow server
+
+        Args:
+            mlflow_tracking_uri: a tracking URI for MLflow server which could be local directory or address of
+                the remote tracking Server; MLflow runs will be recorded locally in algorithms' model folder if
+                the value is None.
+        """
+        self.mlflow_tracking_uri = mlflow_tracking_uri  # type: ignore
+
     def fill_template_config(self, data_stats_filename: str, algo_path: str, **kwargs: Any) -> dict:
         """
         The configuration files defined when constructing this Algo instance might not have a complete training
@@ -432,6 +444,9 @@ class BundleGen(AlgoGen):
         data_stats_filename: the path to the data stats file (generated by DataAnalyzer).
         data_src_cfg_name: the path to the data source config YAML file. The config will be in a form of
                            {"modality": "ct", "datalist": "path_to_json_datalist", "dataroot": "path_dir_data"}.
+        mlflow_tracking_uri: a tracking URI for MLflow server which could be local directory or address of
+            the remote tracking Server; MLflow runs will be recorded locally in algorithms' model folder if
+            the value is None.
     .. code-block:: bash
 
         python -m monai.apps.auto3dseg BundleGen generate --data_stats_filename="../algorithms/datastats.yaml"
@@ -444,6 +459,7 @@ def __init__(
         templates_path_or_url: str | None = None,
         data_stats_filename: str | None = None,
         data_src_cfg_name: str | None = None,
+        mlflow_tracking_uri: str | None = None,
     ):
         if algos is None or isinstance(algos, (list, tuple, str)):
             if templates_path_or_url is None:
@@ -496,6 +512,7 @@ def __init__(
 
         self.data_stats_filename = data_stats_filename
         self.data_src_cfg_name = data_src_cfg_name
+        self.mlflow_tracking_uri = mlflow_tracking_uri
         self.history: list[dict] = []
 
     def set_data_stats(self, data_stats_filename: str) -> None:
@@ -524,6 +541,21 @@ def get_data_src(self):
         """Get the data source filename"""
         return self.data_src_cfg_name
 
+    def set_mlflow_tracking_uri(self, mlflow_tracking_uri):
+        """
+        Set the tracking URI for MLflow server
+
+        Args:
+            mlflow_tracking_uri: a tracking URI for MLflow server which could be local directory or address of
+                the remote tracking Server; MLflow runs will be recorded locally in algorithms' model folder if
+                the value is None.
+        """
+        self.mlflow_tracking_uri = mlflow_tracking_uri
+
+    def get_mlflow_tracking_uri(self):
+        """Get the tracking URI for MLflow server"""
+        return self.mlflow_tracking_uri
+
     def get_history(self) -> list:
         """Get the history of the bundleAlgo object with their names/identifiers"""
         return self.history
@@ -575,9 +607,11 @@ def generate(
             for f_id in ensure_tuple(fold_idx):
                 data_stats = self.get_data_stats()
                 data_src_cfg = self.get_data_src()
+                mlflow_tracking_uri = self.get_mlflow_tracking_uri()
                 gen_algo = deepcopy(algo)
                 gen_algo.set_data_stats(data_stats)
                 gen_algo.set_data_source(data_src_cfg)
+                gen_algo.set_mlflow_tracking_uri(mlflow_tracking_uri)
                 name = f"{gen_algo.name}_{f_id}"
 
                 if allow_skip: