diff --git a/generic_config_updater/change_applier.py b/generic_config_updater/change_applier.py
index 63ca98049c..9871e554b2 100644
--- a/generic_config_updater/change_applier.py
+++ b/generic_config_updater/change_applier.py
@@ -71,6 +71,11 @@ class ChangeApplier:
 
     def __init__(self):
         self.config_db = get_config_db()
+        self.backend_tables = [
+            "BUFFER_PG",
+            "BUFFER_PROFILE",
+            "FLEX_COUNTER_TABLE"
+        ]
         if (not ChangeApplier.updater_conf) and os.path.exists(UPDATER_CONF_FILE):
             with open(UPDATER_CONF_FILE, "r") as s:
                 ChangeApplier.updater_conf = json.load(s)
@@ -142,6 +147,8 @@ def apply(self, change):
         ret = self._services_validate(run_data, upd_data, upd_keys)
         if not ret:
             run_data = self._get_running_config()
+            self.remove_backend_tables_from_config(upd_data)
+            self.remove_backend_tables_from_config(run_data)
             if upd_data != run_data:
                 self._report_mismatch(run_data, upd_data)
                 ret = -1
@@ -150,6 +157,11 @@ def apply(self, change):
         return ret
 
 
+    def remove_backend_tables_from_config(self, data):
+        for key in self.backend_tables:
+            data.pop(key, None)
+
+
     def _get_running_config(self):
         (_, fname) = tempfile.mkstemp(suffix="_changeApplier")
         os.system("sonic-cfggen -d --print-data > {}".format(fname))
diff --git a/generic_config_updater/generic_updater.py b/generic_config_updater/generic_updater.py
index ee7af65620..56297039aa 100644
--- a/generic_config_updater/generic_updater.py
+++ b/generic_config_updater/generic_updater.py
@@ -77,6 +77,8 @@ def apply(self, patch):
         # Validate config updated successfully
         self.logger.log_notice("Verifying patch updates are reflected on ConfigDB.")
         new_config = self.config_wrapper.get_config_db_as_json()
+        self.changeapplier.remove_backend_tables_from_config(target_config)
+        self.changeapplier.remove_backend_tables_from_config(new_config)
         if not(self.patch_wrapper.verify_same_json(target_config, new_config)):
             raise GenericConfigUpdaterError(f"After applying patch to config, there are still some parts not updated")