diff --git a/pr_agent/agent/pr_agent.py b/pr_agent/agent/pr_agent.py
index 476957d5..3d819af5 100644
--- a/pr_agent/agent/pr_agent.py
+++ b/pr_agent/agent/pr_agent.py
@@ -6,7 +6,6 @@ import tempfile
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
-from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.tools.pr_add_docs import PRAddDocs
 from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
 from pr_agent.tools.pr_description import PRDescription
@@ -45,7 +44,22 @@ class PRAgent:
 
     async def handle_request(self, pr_url, request, notify=None) -> bool:
         # First, apply repo specific settings if exists
-        apply_repo_settings(pr_url)
+        if get_settings().config.use_repo_settings_file:
+            repo_settings_file = None
+            try:
+                git_provider = get_git_provider()(pr_url)
+                repo_settings = git_provider.get_repo_settings()
+                if repo_settings:
+                    repo_settings_file = None
+                    fd, repo_settings_file = tempfile.mkstemp(suffix='.toml')
+                    os.write(fd, repo_settings)
+                    get_settings().load_file(repo_settings_file)
+            finally:
+                if repo_settings_file:
+                    try:
+                        os.remove(repo_settings_file)
+                    except Exception as e:
+                        logging.error(f"Failed to remove temporary settings file {repo_settings_file}", e)
 
         # Then, apply user specific settings if exists
         request = request.replace("'", "\\'")
@@ -70,4 +84,3 @@ class PRAgent:
         else:
             return False
         return True
-
diff --git a/pr_agent/git_providers/utils.py b/pr_agent/git_providers/utils.py
deleted file mode 100644
index d2dc79af..00000000
--- a/pr_agent/git_providers/utils.py
+++ /dev/null
@@ -1,35 +0,0 @@
-import copy
-import logging
-import os
-import tempfile
-
-from dynaconf import Dynaconf
-
-from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider
-
-
-def apply_repo_settings(pr_url):
-    if get_settings().config.use_repo_settings_file:
-        repo_settings_file = None
-        try:
-            git_provider = get_git_provider()(pr_url)
-            repo_settings = git_provider.get_repo_settings()
-            if repo_settings:
-                repo_settings_file = None
-                fd, repo_settings_file = tempfile.mkstemp(suffix='.toml')
-                os.write(fd, repo_settings)
-                new_settings = Dynaconf(settings_files=[repo_settings_file])
-                for section, contents in new_settings.as_dict().items():
-                    section_dict = copy.deepcopy(get_settings().as_dict().get(section, {}))
-                    for key, value in contents.items():
-                        section_dict[key] = value
-                    get_settings().unset(section)
-                    get_settings().set(section, section_dict, merge=False)
-
-        finally:
-            if repo_settings_file:
-                try:
-                    os.remove(repo_settings_file)
-                except Exception as e:
-                    logging.error(f"Failed to remove temporary settings file {repo_settings_file}", e)
diff --git a/pr_agent/servers/github_app.py b/pr_agent/servers/github_app.py
index 272d9d0f..c9f25124 100644
--- a/pr_agent/servers/github_app.py
+++ b/pr_agent/servers/github_app.py
@@ -15,7 +15,6 @@ from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.git_providers import get_git_provider
-from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.servers.utils import verify_signature
 
 logging.basicConfig(stream=sys.stdout, level=logging.INFO)
@@ -125,7 +124,6 @@ async def handle_request(body: Dict[str, Any], event: str):
                     # avoid double reviews when opening a PR for the first time
                     return {}
             logging.info(f"Performing review because of event={event} and action={action}")
-            apply_repo_settings(api_url)
             for command in get_settings().github_app.pr_commands:
                 split_command = command.split(" ")
                 command = split_command[0]