diff --git a/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py b/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py
index c0c5d30239b84..5c71a0c501243 100644
--- a/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py
+++ b/datadog_checks_base/datadog_checks/base/checks/prometheus/base_check.py
@@ -147,8 +147,6 @@ def get_scraper(self, instance):
                 metrics_mapper[metric] = metric
             else:
                 metrics_mapper.update(metric)
-        # update metrics mapper with values provided by user
-        metrics_mapper.update(instance.get("metrics_mapper", {}))
 
         scraper.metrics_mapper = metrics_mapper
         scraper.labels_mapper = default_instance.get("labels_mapper", {})