diff --git a/tools/crd-bumper/crd-bumper.py b/tools/crd-bumper/crd-bumper.py
index 1deb02c..0ff2727 100755
--- a/tools/crd-bumper/crd-bumper.py
+++ b/tools/crd-bumper/crd-bumper.py
@@ -335,9 +335,13 @@ def bump_controllers(cgen, makecmd, git, stage, project, args, bumper_cfg):
     controllers.edit_util_conversion_test()
 
     # Bump any other, non-controller, directories of code.
-    if bumper_cfg is not None and 'extra_go_dirs' in bumper_cfg:
+    if bumper_cfg is not None and "extra_go_dirs" in bumper_cfg:
         for extra_dir in bumper_cfg["extra_go_dirs"].split(","):
             controllers.update_extras(extra_dir)
+    # Bump any necessary references in the config/ dir.
+    if bumper_cfg is not None and "extra_config_dirs" in bumper_cfg:
+        for extra_dir in bumper_cfg["extra_config_dirs"].split(","):
+            controllers.update_extra_config(extra_dir)
 
     makecmd.fmt()
     controllers.commit_bump_controllers(git, stage)
diff --git a/tools/crd-bumper/pkg/controllers.py b/tools/crd-bumper/pkg/controllers.py
index 9251b07..b9b4c76 100644
--- a/tools/crd-bumper/pkg/controllers.py
+++ b/tools/crd-bumper/pkg/controllers.py
@@ -104,6 +104,26 @@ def update_extras(self, dirname):
                 if fname.endswith(".go"):
                     self._point_at_new_hub(kinds, full_path)
 
+    def update_extra_config(self, dirname):
+        """Walk over Kustomize config files and bump them to point at the new hub.
+        This is for any resource that may be exposed to ArgoCD, which would would
+        otherwise mark the resource as OutOfSync because the argocd queries will
+        show it with the new hub.
+        """
+
+        kinds = self._project.kinds(self._prev_ver)
+        if len(kinds) == 0:
+            raise ValueError(f"Nothing found at version {self._prev_ver}")
+
+        if os.path.isdir(dirname) is False:
+            raise ValueError(f"{dirname} is not a directory")
+
+        for root, _, f_names in os.walk(dirname, followlinks=False):
+            for fname in f_names:
+                full_path = os.path.join(root, fname)
+                if fname.endswith(".yaml"):
+                    self._point_config_at_new_hub(kinds, full_path)
+
     def _walk_files(self, top, kinds):
         """Walk the files in the given directory, and update them to point at the new hub."""
 
@@ -157,6 +177,24 @@ def _point_at_new_hub(self, kinds, path):
             fu.replace_in_file(f"{group}{self._prev_ver}.", f"{group}{self._new_ver}.")
             fu.store()
 
+    def _point_config_at_new_hub(self, kinds, path):
+        """Update the given file to point it at the new hub."""
+
+        fu = FileUtil(self._dryrun, path)
+
+        if self._preferred_alias is None:
+            # Pick the first kind, use its group.
+            group = self._project.group(kinds[0], self._prev_ver)
+        else:
+            group = self._preferred_alias
+
+        pat = f"apiVersion: {group}"
+        line = fu.find_in_file(pat)
+        if line is not None:
+            line2 = line.replace(self._prev_ver, self._new_ver)
+            fu.replace_in_file(line, line2)
+        fu.store()
+
     def _update_suite_test(self, kinds, path):
         """Update the suite_test.go file to include the setup of the new hub."""
 
diff --git a/tools/crd-bumper/pkg/conversion_gen.py b/tools/crd-bumper/pkg/conversion_gen.py
index 5be249d..0153263 100644
--- a/tools/crd-bumper/pkg/conversion_gen.py
+++ b/tools/crd-bumper/pkg/conversion_gen.py
@@ -102,13 +102,6 @@ def fix_kubebuilder_import_alias(self):
         )
         fu.store()
 
-        # for root, _, f_names in os.walk(f"api/{self._new_ver}", followlinks=False):
-        #  for fname in f_names:
-        #    full_path = os.path.join(root, fname)
-        #    fu = FileUtil(self._dryrun, full_path)
-        #    fu.replace_in_file(f"{group}{self._new_ver}", f"{self._preferred_alias}{self._new_ver}")
-        #    fu.store()
-
     def module(self):
         """Return the name of this Go module."""
 
@@ -389,6 +382,7 @@ def mk_spoke_fuzz_test(self):
             fu.append(template)
 
         # Wake up!  Multi-line f-string:
+        # pylint: disable=f-string-without-interpolation
         template = f"""
 }}