diff --git a/tests/data/test_config.yaml b/tests/data/test_config.yaml
index 42f4f6f7bb992..5090e8f357bb8 100644
--- a/tests/data/test_config.yaml
+++ b/tests/data/test_config.yaml
@@ -1,3 +1,5 @@
 port: 12312
 served_model_name: mymodel
 tensor_parallel_size: 2
+trust_remote_code: true
+multi_step_stream_outputs: false
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 0fed8e678fc76..a731b11eae81c 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -6,7 +6,7 @@
 
 import pytest
 
-from vllm.utils import (FlexibleArgumentParser, deprecate_kwargs,
+from vllm.utils import (FlexibleArgumentParser, StoreBoolean, deprecate_kwargs,
                         get_open_port, merge_async_iterators, supports_kw)
 
 from .utils import error_on_warning
@@ -141,6 +141,8 @@ def parser_with_config():
     parser.add_argument('--config', type=str)
     parser.add_argument('--port', type=int)
     parser.add_argument('--tensor-parallel-size', type=int)
+    parser.add_argument('--trust-remote-code', action='store_true')
+    parser.add_argument('--multi-step-stream-outputs', action=StoreBoolean)
     return parser
 
 
@@ -214,6 +216,8 @@ def test_config_args(parser_with_config):
     args = parser_with_config.parse_args(
         ['serve', 'mymodel', '--config', './data/test_config.yaml'])
     assert args.tensor_parallel_size == 2
+    assert args.trust_remote_code
+    assert not args.multi_step_stream_outputs
 
 
 def test_config_file(parser_with_config):
diff --git a/vllm/engine/arg_utils.py b/vllm/engine/arg_utils.py
index c49f475b9ee61..38687809a31f6 100644
--- a/vllm/engine/arg_utils.py
+++ b/vllm/engine/arg_utils.py
@@ -19,7 +19,7 @@
 from vllm.transformers_utils.config import (
     maybe_register_config_serialize_by_value)
 from vllm.transformers_utils.utils import check_gguf_file
-from vllm.utils import FlexibleArgumentParser
+from vllm.utils import FlexibleArgumentParser, StoreBoolean
 
 if TYPE_CHECKING:
     from vllm.transformers_utils.tokenizer_group import BaseTokenizerGroup
@@ -1144,18 +1144,6 @@ def add_cli_args(parser: FlexibleArgumentParser,
         return parser
 
 
-class StoreBoolean(argparse.Action):
-
-    def __call__(self, parser, namespace, values, option_string=None):
-        if values.lower() == "true":
-            setattr(namespace, self.dest, True)
-        elif values.lower() == "false":
-            setattr(namespace, self.dest, False)
-        else:
-            raise ValueError(f"Invalid boolean value: {values}. "
-                             "Expected 'true' or 'false'.")
-
-
 # These functions are used by sphinx to build the documentation
 def _engine_args_parser():
     return EngineArgs.add_cli_args(FlexibleArgumentParser())
diff --git a/vllm/utils.py b/vllm/utils.py
index fba9804289b94..ac27b1ac4ab2d 100644
--- a/vllm/utils.py
+++ b/vllm/utils.py
@@ -1155,6 +1155,18 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> None:
     return wrapper
 
 
+class StoreBoolean(argparse.Action):
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        if values.lower() == "true":
+            setattr(namespace, self.dest, True)
+        elif values.lower() == "false":
+            setattr(namespace, self.dest, False)
+        else:
+            raise ValueError(f"Invalid boolean value: {values}. "
+                             "Expected 'true' or 'false'.")
+
+
 class FlexibleArgumentParser(argparse.ArgumentParser):
     """ArgumentParser that allows both underscore and dash in names."""
 
@@ -1163,7 +1175,7 @@ def parse_args(self, args=None, namespace=None):
             args = sys.argv[1:]
 
         if '--config' in args:
-            args = FlexibleArgumentParser._pull_args_from_config(args)
+            args = self._pull_args_from_config(args)
 
         # Convert underscores to dashes and vice versa in argument names
         processed_args = []
@@ -1181,8 +1193,7 @@ def parse_args(self, args=None, namespace=None):
 
         return super().parse_args(processed_args, namespace)
 
-    @staticmethod
-    def _pull_args_from_config(args: List[str]) -> List[str]:
+    def _pull_args_from_config(self, args: List[str]) -> List[str]:
         """Method to pull arguments specified in the config file
         into the command-line args variable.
 
@@ -1226,7 +1237,7 @@ def _pull_args_from_config(args: List[str]) -> List[str]:
 
         file_path = args[index + 1]
 
-        config_args = FlexibleArgumentParser._load_config_file(file_path)
+        config_args = self._load_config_file(file_path)
 
         # 0th index is for {serve,chat,complete}
         # followed by model_tag (only for serve)
@@ -1247,8 +1258,7 @@ def _pull_args_from_config(args: List[str]) -> List[str]:
 
         return args
 
-    @staticmethod
-    def _load_config_file(file_path: str) -> List[str]:
+    def _load_config_file(self, file_path: str) -> List[str]:
         """Loads a yaml file and returns the key value pairs as a
         flattened list with argparse like pattern
         ```yaml
@@ -1282,9 +1292,18 @@ def _load_config_file(file_path: str) -> List[str]:
                 Make sure path is correct", file_path)
             raise ex
 
+        store_boolean_arguments = [
+            action.dest for action in self._actions
+            if isinstance(action, StoreBoolean)
+        ]
+
         for key, value in config.items():
-            processed_args.append('--' + key)
-            processed_args.append(str(value))
+            if isinstance(value, bool) and key not in store_boolean_arguments:
+                if value:
+                    processed_args.append('--' + key)
+            else:
+                processed_args.append('--' + key)
+                processed_args.append(str(value))
 
         return processed_args