diff --git a/monai/apps/nnunet/nnunetv2_runner.py b/monai/apps/nnunet/nnunetv2_runner.py
index 547e73332f..8d9c80f044 100644
--- a/monai/apps/nnunet/nnunetv2_runner.py
+++ b/monai/apps/nnunet/nnunetv2_runner.py
@@ -596,9 +596,17 @@ def train_single_model_command(
         if self.export_validation_probabilities:
             cmd.append("--npz")
 
+        store_true_flags = {"c", "val", "use_compressed", "disable_checkpointing"}
         for _key, _value in kwargs.items():
             prefix = "-" if _key in {"p", "pretrained_weights"} else "--"
-            cmd += [f"{prefix}{_key}", str(_value)]
+            if _key in store_true_flags:
+                if _value:
+                    cmd.append(f"{prefix}{_key}")
+            elif _key in {"p", "pretrained_weights"}:
+                if _value:
+                    cmd += [f"{prefix}{_key}", str(_value)]
+            else:
+                cmd += [f"{prefix}{_key}", str(_value)]
 
         cmd_str: list[str] = [str(c) for c in cmd]
 
@@ -758,7 +766,7 @@ def validate_single_model(self, config: str, fold: int, **kwargs: Any) -> None:
             kwargs: this optional parameter allows you to specify additional arguments defined in the
                 ``train_single_model`` method.
         """
-        self.train_single_model(config=config, fold=fold, only_run_validation=True, **kwargs)
+        self.train_single_model(config=config, fold=fold, val=True, **kwargs)
 
     def validate(
         self, configs: tuple = (M.N_3D_FULLRES, M.N_2D, M.N_3D_LOWRES, M.N_3D_CASCADE_FULLRES), **kwargs: Any
diff --git a/tests/apps/nnunet/__init__.py b/tests/apps/nnunet/__init__.py
new file mode 100644
index 0000000000..1e97f89407
--- /dev/null
+++ b/tests/apps/nnunet/__init__.py
@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
diff --git a/tests/apps/nnunet/test_nnunetv2_runner_command.py b/tests/apps/nnunet/test_nnunetv2_runner_command.py
new file mode 100644
index 0000000000..506c30fad0
--- /dev/null
+++ b/tests/apps/nnunet/test_nnunetv2_runner_command.py
@@ -0,0 +1,78 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import unittest
+from unittest import mock
+
+from monai.apps.nnunet.nnunetv2_runner import nnUNetV2Runner
+
+
+def _make_runner(export_validation_probabilities=False):
+    runner = nnUNetV2Runner.__new__(nnUNetV2Runner)
+    runner.dataset_name_or_id = "001"
+    runner.trainer_class_name = "nnUNetTrainer"
+    runner.export_validation_probabilities = export_validation_probabilities
+    return runner
+
+
+class TestTrainSingleModelCommand(unittest.TestCase):
+    def test_store_true_flags_emit_bare(self):
+        runner = _make_runner()
+        cmd, _ = runner.train_single_model_command(
+            "3d_fullres", 0, 0, {"c": True, "val": True, "use_compressed": True, "disable_checkpointing": True}
+        )
+        for flag in ("--c", "--val", "--use_compressed", "--disable_checkpointing"):
+            self.assertIn(flag, cmd)
+        self.assertNotIn("True", cmd)
+
+    def test_store_true_flags_false_omitted(self):
+        runner = _make_runner()
+        cmd, _ = runner.train_single_model_command(
+            "3d_fullres", 0, 0, {"c": False, "val": False, "use_compressed": False, "disable_checkpointing": False}
+        )
+        for flag in ("--c", "--val", "--use_compressed", "--disable_checkpointing"):
+            self.assertNotIn(flag, cmd)
+        self.assertNotIn("False", cmd)
+
+    def test_pretrained_weights_truthy_included(self):
+        runner = _make_runner()
+        cmd, _ = runner.train_single_model_command("3d_fullres", 0, 0, {"pretrained_weights": "/path/to/weights.pth"})
+        self.assertIn("-pretrained_weights", cmd)
+        self.assertIn("/path/to/weights.pth", cmd)
+
+    def test_pretrained_weights_falsy_omitted(self):
+        runner = _make_runner()
+        cmd, _ = runner.train_single_model_command("3d_fullres", 0, 0, {"pretrained_weights": False})
+        self.assertNotIn("-pretrained_weights", cmd)
+        self.assertNotIn("False", cmd)
+
+    def test_value_kwargs_unaffected(self):
+        runner = _make_runner()
+        cmd, _ = runner.train_single_model_command("3d_fullres", 0, 0, {"npz": "something"})
+        self.assertIn("--npz", cmd)
+        self.assertIn("something", cmd)
+
+
+class TestValidateSingleModelCommand(unittest.TestCase):
+    def test_validate_emits_bare_val_flag(self):
+        runner = _make_runner()
+        with mock.patch("monai.apps.nnunet.nnunetv2_runner.run_cmd") as run_cmd:
+            runner.validate_single_model("3d_fullres", 0)
+        cmd = run_cmd.call_args.args[0]
+        self.assertIn("--val", cmd)
+        self.assertNotIn("--only_run_validation", cmd)
+        self.assertNotIn("True", cmd)
+
+
+if __name__ == "__main__":
+    unittest.main()