diff --git a/server/common/app_config.py b/server/common/app_config.py
index e0a49e46..3102bae0 100644
--- a/server/common/app_config.py
+++ b/server/common/app_config.py
@@ -95,8 +95,10 @@ class AppConfig(object):
         with open(config_file) as fyaml:
             config = yaml.load(fyaml, Loader=yaml.FullLoader)
 
-        self.server_config.update_from_config(config["server"], "server")
-        self.default_dataset_config.update_from_config(config["dataset"], "dataset")
+        if config.get("server"):
+            self.server_config.update_from_config(config["server"], "server")
+        if config.get("dataset"):
+            self.default_dataset_config.update_from_config(config["dataset"], "dataset")
 
         per_dataset_config = config.get("per_dataset_config", {})
         for key, dataroot_config in per_dataset_config.items():
diff --git a/server/test/unit/common/test_app_config.py b/server/test/unit/common/test_app_config.py
index 6b86d771..c3dd1436 100644
--- a/server/test/unit/common/test_app_config.py
+++ b/server/test/unit/common/test_app_config.py
@@ -206,3 +206,44 @@ class AppConfigTest(unittest.TestCase):
 
             # test config from specialization
             self.assertTrue(test_config.user_annotations__enable)
+
+    def test_configfile_no_dataset_section(self):
+        # test a config file without a dataset section
+
+        with tempfile.TemporaryDirectory() as tempdir:
+            configfile = os.path.join(tempdir, "config.yaml")
+            with open(configfile, "w") as fconfig:
+                config = """
+                server:
+                    multi_dataset:
+                        dataroot: test_dataroot
+
+                """
+                fconfig.write(config)
+
+            app_config = AppConfig()
+            app_config.update_from_config_file(configfile)
+            server_changes = app_config.server_config.changes_from_default()
+            dataset_changes = app_config.default_dataset_config.changes_from_default()
+            self.assertEqual(server_changes, [("multi_dataset__dataroot", "test_dataroot", None)])
+            self.assertEqual(dataset_changes, [])
+
+    def test_configfile_no_server_section(self):
+        # test a config file without a dataset section
+
+        with tempfile.TemporaryDirectory() as tempdir:
+            configfile = os.path.join(tempdir, "config.yaml")
+            with open(configfile, "w") as fconfig:
+                config = """
+                dataset:
+                    user_annotations:
+                        enable: false
+                """
+                fconfig.write(config)
+
+            app_config = AppConfig()
+            app_config.update_from_config_file(configfile)
+            server_changes = app_config.server_config.changes_from_default()
+            dataset_changes = app_config.default_dataset_config.changes_from_default()
+            self.assertEqual(server_changes, [])
+            self.assertEqual(dataset_changes, [("user_annotations__enable", False, True)])