diff --git a/frappe/installer.py b/frappe/installer.py
index 471a59bc00..f3c50659af 100644
--- a/frappe/installer.py
+++ b/frappe/installer.py
@@ -539,7 +539,6 @@ def make_site_config(
 			f.write(json.dumps(site_config, indent=1, sort_keys=True))
 
 
-@filelock("site_config")
 def update_site_config(key, value, validate=True, site_config_path=None):
 	"""Update a value in site_config"""
 	from frappe.utils.synchronization import filelock
@@ -547,7 +546,16 @@ def update_site_config(key, value, validate=True, site_config_path=None):
 	if not site_config_path:
 		site_config_path = get_site_config_path()
 
-	with open(site_config_path) as f:
+	# Sometimes global config file is passed directly to this function
+	_is_global_conf = "common_site_config" in site_config_path
+
+	with filelock("site_config", is_global=_is_global_conf):
+		_update_config_file(key=key, value=value, config_file=site_config_path)
+
+
+def _update_config_file(key: str, value, config_file: str):
+	"""Updates site or common config"""
+	with open(config_file) as f:
 		site_config = json.loads(f.read())
 
 	# In case of non-int value
@@ -567,7 +575,7 @@ def update_site_config(key, value, validate=True, site_config_path=None):
 	else:
 		site_config[key] = value
 
-	with open(site_config_path, "w") as f:
+	with open(config_file, "w") as f:
 		f.write(json.dumps(site_config, indent=1, sort_keys=True))
 
 	if hasattr(frappe.local, "conf"):
diff --git a/frappe/tests/test_commands.py b/frappe/tests/test_commands.py
index 343184d01a..6582b29b7e 100644
--- a/frappe/tests/test_commands.py
+++ b/frappe/tests/test_commands.py
@@ -479,6 +479,14 @@ class TestCommands(BaseTestCommands):
 		self.assertIn(f"Installing {app_name}", self.stdout)
 		self.assertEqual(self.returncode, 0)
 
+	def test_set_global_conf(self):
+		key = "answer"
+		value = "42"
+		self.execute(f"bench set-config {key} {value} -g")
+		conf = frappe.get_site_config()
+
+		self.assertEqual(conf[key], value)
+
 
 class TestBackups(BaseTestCommands):
 	backup_map = {