diff --git a/.github/styles/vocab.txt b/.github/styles/vocab.txt
index fea996b03b..6359493d4b 100644
--- a/.github/styles/vocab.txt
+++ b/.github/styles/vocab.txt
@@ -278,6 +278,8 @@ sqlite
 squidfunk
 src
 stdout
+stringify
+stringified
 subcomponent
 subcomponents
 subkey
diff --git a/plugins/catalog-backend/migrations/20220222164811_reprocess_for_relation_refs.js b/plugins/catalog-backend/migrations/20220222164811_reprocess_for_relation_refs.js
new file mode 100644
index 0000000000..f4be2172a0
--- /dev/null
+++ b/plugins/catalog-backend/migrations/20220222164811_reprocess_for_relation_refs.js
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2021 The Backstage Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+// @ts-check
+
+/**
+ * @param {import('knex').Knex} knex
+ */
+exports.up = async function up(knex) {
+  // Make sure to reprocess everything, to make sure that relations have a targetRef produced
+  await knex('refresh_state').update({
+    result_hash: '',
+    next_update_at: knex.fn.now(),
+  });
+  await knex('final_entities').update({ hash: '' });
+};
+
+exports.down = async function down() {};
diff --git a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
index 3b20282d78..f8b68bebc5 100644
--- a/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
+++ b/plugins/catalog-backend/src/service/DefaultEntitiesCatalog.ts
@@ -211,11 +211,11 @@ export class DefaultEntitiesCatalog implements EntitiesCatalog {
     for (const entity of entities) {
       if (entity.relations) {
         for (const relation of entity.relations) {
-          if (!relation.targetRef) {
+          if (!relation.targetRef && relation.target) {
             // This is the case where an old-form entity, not yet stitched with
             // the updated code, was in the database
             relation.targetRef = stringifyEntityRef(relation.target);
-          } else if (!relation.target) {
+          } else if (!relation.target && relation.targetRef) {
             // This is the case where a new-form entity, stitched with the
             // updated code, was in the database but we still want to produce
             // the old data shape as well for compatibility reasons
diff --git a/plugins/catalog-backend/src/stitching/Stitcher.ts b/plugins/catalog-backend/src/stitching/Stitcher.ts
index 018e223e46..37b86fef46 100644
--- a/plugins/catalog-backend/src/stitching/Stitcher.ts
+++ b/plugins/catalog-backend/src/stitching/Stitcher.ts
@@ -18,6 +18,7 @@ import { ENTITY_STATUS_CATALOG_PROCESSING_TYPE } from '@backstage/catalog-client
 import {
   AlphaEntity,
   parseEntityRef,
+  EntityRelation,
   EntityStatusItem,
 } from '@backstage/catalog-model';
 import { SerializedError, stringifyError } from '@backstage/errors';
@@ -183,8 +184,9 @@ export class Stitcher {
     );
     entity.relations = uniqueRelationRows
       .filter(row => row.relationType /* exclude null row, if relevant */)
-      .map(row => ({
+      .map<EntityRelation>(row => ({
         type: row.relationType!,
+        // TODO(freben): This field is deprecated and should be removed in a future release
         target: parseEntityRef(row.relationTarget!),
         targetRef: row.relationTarget!,
       }));