diff --git a/hack/update-codegen.sh b/hack/update-codegen.sh
index 7ead9d63d5c..d6112d00efa 100755
--- a/hack/update-codegen.sh
+++ b/hack/update-codegen.sh
@@ -594,6 +594,12 @@ function codegen::applyconfigs() {
         done
     fi
 
+    git_grep -l --null \
+        -e '^// Code generated by applyconfiguration-gen. DO NOT EDIT.$' \
+        -- \
+        ':(glob)staging/src/k8s.io/client-go/**/*.go' \
+        | xargs -0 rm -f
+
     "${applyconfigurationgen}" \
         --openapi-schema <("${modelsschema}") \
         --go-header-file "${BOILERPLATE_FILENAME}" \