diff --git a/pr_agent/servers/bitbucket_app.py b/pr_agent/servers/bitbucket_app.py
index a0384da14..8701463df 100644
--- a/pr_agent/servers/bitbucket_app.py
+++ b/pr_agent/servers/bitbucket_app.py
@@ -75,8 +75,11 @@ async def handle_manifest(request: Request, response: Response):
     return JSONResponse(manifest_obj)
 
 
-async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict):
+async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict, data: dict):
     apply_repo_settings(api_url)
+    if data.get("event", "") == "pullrequest:created":
+        if not should_process_pr_logic(data):
+            return
     commands = get_settings().get(f"bitbucket_app.{commands_conf}", {})
     get_settings().set("config.is_auto_command", True)
     for command in commands:
@@ -193,7 +196,7 @@ async def inner():
                         if get_identity_provider().verify_eligibility("bitbucket",
                                                         sender_id, pr_url) is not Eligibility.NOT_ELIGIBLE:
                             if get_settings().get("bitbucket_app.pr_commands"):
-                                await _perform_commands_bitbucket("pr_commands", PRAgent(), pr_url, log_context)
+                                await _perform_commands_bitbucket("pr_commands", PRAgent(), pr_url, log_context, data)
             elif event == "pullrequest:comment_created":
                 pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
                 log_context["api_url"] = pr_url
diff --git a/pr_agent/servers/github_app.py b/pr_agent/servers/github_app.py
index 00da88e35..728d72c16 100644
--- a/pr_agent/servers/github_app.py
+++ b/pr_agent/servers/github_app.py
@@ -249,7 +249,7 @@ def is_bot_user(sender, sender_type):
     return False
 
 
-def should_process_pr_logic(sender_type, sender, body) -> bool:
+def should_process_pr_logic(body) -> bool:
     try:
         pull_request = body.get("pull_request", {})
         title = pull_request.get("title", "")
@@ -306,10 +306,10 @@ async def handle_request(body: Dict[str, Any], event: str):
     log_context, sender, sender_id, sender_type = get_log_context(body, event, action, build_number)
 
     # logic to ignore PRs opened by bot, PRs with specific titles, labels, source branches, or target branches
-    if is_bot_user(sender, sender_type):
+    if is_bot_user(sender, sender_type) and 'check_run' not in body:
         return {}
     if action != 'created' and 'check_run' not in body:
-        if not should_process_pr_logic(sender_type, sender, body):
+        if not should_process_pr_logic(body):
             return {}
 
     if 'check_run' in body:  # handle failed checks
@@ -373,6 +373,8 @@ def _check_pull_request_event(action: str, body: dict, log_context: dict) -> Tup
 async def _perform_auto_commands_github(commands_conf: str, agent: PRAgent, body: dict, api_url: str,
                                         log_context: dict):
     apply_repo_settings(api_url)
+    if not should_process_pr_logic(body): # Here we already updated the configuration with the repo settings
+        return {}
     commands = get_settings().get(f"github_app.{commands_conf}")
     if not commands:
         get_logger().info(f"New PR, but no auto commands configured")
diff --git a/pr_agent/servers/gitlab_webhook.py b/pr_agent/servers/gitlab_webhook.py
index 15d4fa418..d8bdb2f7a 100644
--- a/pr_agent/servers/gitlab_webhook.py
+++ b/pr_agent/servers/gitlab_webhook.py
@@ -59,8 +59,10 @@ async def handle_request(api_url: str, body: str, log_context: dict, sender_id:
 
 
 async def _perform_commands_gitlab(commands_conf: str, agent: PRAgent, api_url: str,
-                                   log_context: dict):
+                                   log_context: dict, data: dict):
     apply_repo_settings(api_url)
+    if not should_process_pr_logic(data): # Here we already updated the configurations
+        return
     commands = get_settings().get(f"gitlab.{commands_conf}", {})
     get_settings().set("config.is_auto_command", True)
     for command in commands:
@@ -90,8 +92,12 @@ def is_bot_user(data) -> bool:
     return False
 
 
-def should_process_pr_logic(data, title) -> bool:
+def should_process_pr_logic(data) -> bool:
     try:
+        if not data.get('object_attributes', {}):
+            return False
+        title = data['object_attributes'].get('title')
+
         # logic to ignore MRs for titles, labels and source, target branches.
         ignore_mr_title = get_settings().get("CONFIG.IGNORE_PR_TITLE", [])
         ignore_mr_labels = get_settings().get("CONFIG.IGNORE_PR_LABELS", [])
@@ -173,9 +179,9 @@ async def inner(data: dict):
         # ignore bot users
         if is_bot_user(data):
             return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
-        if data.get('event_type') != 'note' and data.get('object_attributes', {}): # not a comment
+        if data.get('event_type') != 'note': # not a comment
             # ignore MRs based on title, labels, source and target branches
-            if not should_process_pr_logic(data, data['object_attributes'].get('title')):
+            if not should_process_pr_logic(data):
                 return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
         log_context["sender"] = sender
@@ -220,7 +226,7 @@ async def inner(data: dict):
                                         content=jsonable_encoder({"message": "success"}))
 
                 get_logger().debug(f'A push event has been received: {url}')
-                await _perform_commands_gitlab("push_commands", PRAgent(), url, log_context)
+                await _perform_commands_gitlab("push_commands", PRAgent(), url, log_context, data)
             except Exception as e:
                 get_logger().error(f"Failed to handle push event: {e}")