diff --git a/changelogs/unreleased/65278-fix-puma-master-counter-wipe.yml b/changelogs/unreleased/65278-fix-puma-master-counter-wipe.yml
new file mode 100644
index 00000000000..fb9d6fa251d
--- /dev/null
+++ b/changelogs/unreleased/65278-fix-puma-master-counter-wipe.yml
@@ -0,0 +1,5 @@
+---
+title: Fix active metric files being wiped after the app starts
+merge_request: 31668
+author:
+type: fixed
diff --git a/config.ru b/config.ru
index 6f6fb85d8fa..d3c6e304998 100644
--- a/config.ru
+++ b/config.ru
@@ -17,7 +17,22 @@ end
 
 require ::File.expand_path('../config/environment', __FILE__)
 
+
+# The following is necessary to ensure stale Prometheus metrics don't accumulate over time.
+# It needs to be done as early as here to ensure metrics files aren't deleted.
+# After we hit our app in `warmup`, first metrics and corresponding files already being created,
+# for example in `lib/gitlab/metrics/requests_rack_middleware.rb`.
+def cleanup_prometheus_multiproc_dir
+  if dir = ::Prometheus::Client.configuration.multiprocess_files_dir
+    old_metrics = Dir[File.join(dir, '*.db')]
+
+    FileUtils.rm_rf(old_metrics)
+  end
+end
+
 warmup do |app|
+  cleanup_prometheus_multiproc_dir
+
   client = Rack::MockRequest.new(app)
   client.get('/')
 end
diff --git a/config/initializers/7_prometheus_metrics.rb b/config/initializers/7_prometheus_metrics.rb
index 3f2691dde95..70e5dcd042e 100644
--- a/config/initializers/7_prometheus_metrics.rb
+++ b/config/initializers/7_prometheus_metrics.rb
@@ -51,22 +51,3 @@ if !Rails.env.test? && Gitlab::Metrics.prometheus_metrics_enabled?
     end
   end
 end
-
-def cleanup_prometheus_multiproc_dir
-  # The following is necessary to ensure stale Prometheus metrics don't
-  # accumulate over time. It needs to be done in this hook as opposed to
-  # inside an init script to ensure metrics files aren't deleted after new
-  # unicorn workers start after a SIGUSR2 is received.
-  if dir = ::Prometheus::Client.configuration.multiprocess_files_dir
-    old_metrics = Dir[File.join(dir, '*.db')]
-    FileUtils.rm_rf(old_metrics)
-  end
-end
-
-Gitlab::Cluster::LifecycleEvents.on_master_start do
-  cleanup_prometheus_multiproc_dir
-end
-
-Gitlab::Cluster::LifecycleEvents.on_master_restart do
-  cleanup_prometheus_multiproc_dir
-end