diff --git a/lib/config/__snapshots__/migration.spec.ts.snap b/lib/config/__snapshots__/migration.spec.ts.snap
index 7713dfac4bc167..f1833e7c0c0b79 100644
--- a/lib/config/__snapshots__/migration.spec.ts.snap
+++ b/lib/config/__snapshots__/migration.spec.ts.snap
@@ -1,5 +1,37 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`config/migration it migrates nested packageRules 1`] = `
+Object {
+  "packageRules": Array [
+    Object {
+      "enabled": false,
+      "matchDepTypes": Array [
+        "devDependencies",
+      ],
+    },
+    Object {
+      "automerge": true,
+      "excludePackageNames": Array [
+        "@types/react-table",
+      ],
+      "groupName": "definitelyTyped",
+      "matchPackagePrefixes": Array [
+        "@types/",
+      ],
+    },
+    Object {
+      "automerge": false,
+      "excludePackageNames": Array [
+        "@types/react-table",
+      ],
+      "matchDepTypes": Array [
+        "dependencies",
+      ],
+    },
+  ],
+}
+`;
+
 exports[`config/migration migrateConfig(config, parentConfig) does not migrate multi days 1`] = `
 Object {
   "schedule": "after 5:00pm on wednesday and thursday",
@@ -173,6 +205,15 @@ Object {
       ],
       "versioning": "maven",
     },
+    Object {
+      "automerge": true,
+      "matchDepTypes": Array [
+        "bar",
+      ],
+      "matchPackageNames": Array [
+        "foo",
+      ],
+    },
     Object {
       "matchDepTypes": Array [
         "peerDependencies",
@@ -204,15 +245,6 @@ Object {
       "respectLatest": false,
       "schedule": "before 5am on Monday",
     },
-    Object {
-      "automerge": true,
-      "matchDepTypes": Array [
-        "bar",
-      ],
-      "matchPackageNames": Array [
-        "foo",
-      ],
-    },
   ],
   "patch": Object {
     "automerge": true,
diff --git a/lib/config/migration.spec.ts b/lib/config/migration.spec.ts
index dfa75a1599f4b6..29fffe448efd68 100644
--- a/lib/config/migration.spec.ts
+++ b/lib/config/migration.spec.ts
@@ -628,4 +628,35 @@ describe(getName(), () => {
       expect(migratedConfig).toMatchSnapshot();
     });
   });
+  it('it migrates nested packageRules', () => {
+    const config: RenovateConfig = {
+      packageRules: [
+        {
+          matchDepTypes: ['devDependencies'],
+          enabled: false,
+        },
+        {
+          automerge: true,
+          excludePackageNames: ['@types/react-table'],
+          packageRules: [
+            {
+              groupName: 'definitelyTyped',
+              matchPackagePrefixes: ['@types/'],
+            },
+            {
+              matchDepTypes: ['dependencies'],
+              automerge: false,
+            },
+          ],
+        },
+      ],
+    };
+    const { isMigrated, migratedConfig } = configMigration.migrateConfig(
+      config,
+      defaultConfig
+    );
+    expect(isMigrated).toBe(true);
+    expect(migratedConfig).toMatchSnapshot();
+    expect(migratedConfig.packageRules).toHaveLength(3);
+  });
 });
diff --git a/lib/config/migration.ts b/lib/config/migration.ts
index 44e7842cc2fbad..908448c0c10d0c 100644
--- a/lib/config/migration.ts
+++ b/lib/config/migration.ts
@@ -554,7 +554,9 @@ export function migrateConfig(
     }
     // Migrate nested packageRules
     if (is.nonEmptyArray(migratedConfig.packageRules)) {
-      for (const packageRule of migratedConfig.packageRules) {
+      const existingRules = migratedConfig.packageRules;
+      migratedConfig.packageRules = [];
+      for (const packageRule of existingRules) {
         if (is.array(packageRule.packageRules)) {
           logger.debug('Flattening nested packageRules');
           // merge each subrule and add to the parent list
@@ -563,22 +565,10 @@ export function migrateConfig(
             delete combinedRule.packageRules;
             migratedConfig.packageRules.push(combinedRule);
           }
-          // delete the nested packageRules
-          delete packageRule.packageRules;
-          // mark the original rule for deletion if it's now pointless
-          if (
-            !Object.keys(packageRule).some(
-              (key) => !key.startsWith('match') && !key.startsWith('exclude')
-            )
-          ) {
-            packageRule._delete = true;
-          }
+        } else {
+          migratedConfig.packageRules.push(packageRule);
         }
       }
-      // filter out any rules which were marked for deletion in the previous step
-      migratedConfig.packageRules = migratedConfig.packageRules.filter(
-        (rule) => !rule._delete
-      );
     }
     const isMigrated = !dequal(config, migratedConfig);
     if (isMigrated) {