diff --git a/changelog/fragments/fix.yaml b/changelog/fragments/fix.yaml
new file mode 100644
index 0000000000..6dcf881744
--- /dev/null
+++ b/changelog/fragments/fix.yaml
@@ -0,0 +1,8 @@
+# entries is a list of entries to include in
+# release notes and/or the migration guide
+entries:
+  - description: >
+      Fix operator-sdk generate kustomize manifests to respect changes made by users in the config/manifests
+    kind: "bugfix"
+    breaking: false
+
diff --git a/internal/plugins/manifests/v2/templates/config/manifests/kustomization.go b/internal/plugins/manifests/v2/templates/config/manifests/kustomization.go
index 7e7b090a80..87c6122d72 100644
--- a/internal/plugins/manifests/v2/templates/config/manifests/kustomization.go
+++ b/internal/plugins/manifests/v2/templates/config/manifests/kustomization.go
@@ -36,6 +36,12 @@ func (f *Kustomization) SetTemplateDefaults() error {
 		f.Path = filepath.Join("config", "manifests", "kustomization.yaml")
 	}
 
+	// We cannot overwiting the file after it be created because
+	// it might contain user changes (i.e to work with Kustomize 4.x
+	// the target /spec/template/spec/containers/1/volumeMounts/0
+	// needs to be replaced with /spec/template/spec/containers/0/volumeMounts/0
+	f.IfExistsAction = machinery.SkipFile
+
 	f.TemplateBody = kustomizationTemplate
 
 	return nil
diff --git a/website/content/en/docs/faqs/_index.md b/website/content/en/docs/faqs/_index.md
index 35aff6aacb..2adc81dff9 100644
--- a/website/content/en/docs/faqs/_index.md
+++ b/website/content/en/docs/faqs/_index.md
@@ -331,5 +331,19 @@ Here are a couple workarounds to try to resolve the issue:
 
 If neither of those solutions work for you, please [open an issue][open-issue]
 
+## After updating my project to use a Kustomize 4.x version, 'make bundle' does not work
+
+**Valid only for Golang/Hybrid projects using webhooks**
+
+> `Error: remove operation does not apply:doc is missing path: "/spec/template/spec/containers/1/volumeMounts/0": missing value` 
+
+The error occurs due to a change in the Kustomize 4.x versions where the containers used in the Deployment spec of your CSV
+are no longer added at the same order. To sort it out you can update replace the target `/spec/template/spec/containers/1/volumeMounts/0`
+with `/spec/template/spec/containers/0/volumeMounts/0` in `config/manifest/kustomization.yaml`.
+
+**NOTE** You MUST use SDK CLI versions > 1.22. Previous versions have a bug 
+where the command `operator-sdk generate kustomize manifests` is not respecting the changes
+made on this manifest. 
+
 [cgo-docs]: https://pkg.go.dev/cmd/cgo
 [open-issue]: https://github.com/operator-framework/operator-sdk/issues/new/choose
\ No newline at end of file