diff --git a/pkg/kinflate/app/application.go b/pkg/kinflate/app/application.go
index 083ae2fe8..99cdc1091 100644
--- a/pkg/kinflate/app/application.go
+++ b/pkg/kinflate/app/application.go
@@ -83,6 +83,16 @@ func (a *applicationImpl) Resources() (types.ResourceCollection, error) {
 	} else {
 		resources = append(resources, secrets...)
 	}
+	res, err := resourceCollectionFromResources(resources)
+	if err != nil {
+		return nil, err
+	}
+	// Only append hash for generated configmaps and secrets.
+	nht := transformers.NewNameHashTransformer()
+	err = nht.Transform(types.KObject(res))
+	if err != nil {
+		return nil, err
+	}
 
 	ps, err := resource.NewFromPaths(a.loader, a.manifest.Patches)
 	if err != nil {
@@ -98,11 +108,7 @@ func (a *applicationImpl) Resources() (types.ResourceCollection, error) {
 		return nil, errs
 	}
 
-	allResources, err := resourceCollectionFromResources(resources)
-	if err != nil {
-		return nil, err
-	}
-	err = types.Merge(allResources, raw)
+	err = types.Merge(res, raw)
 	if err != nil {
 		return nil, err
 	}
@@ -111,11 +117,11 @@ func (a *applicationImpl) Resources() (types.ResourceCollection, error) {
 	if err != nil {
 		return nil, err
 	}
-	err = t.Transform(types.KObject(allResources))
+	err = t.Transform(types.KObject(res))
 	if err != nil {
 		return nil, err
 	}
-	return allResources, nil
+	return res, nil
 }
 
 // RawResources computes and returns the raw resources from the manifest.
@@ -164,18 +170,14 @@ func (a *applicationImpl) subAppResources() (types.ResourceCollection, *interror
 }
 
 // getTransformer generates the following transformers:
-// 1) append hash for configmaps ans secrets
-// 2) apply overlay
-// 3) name prefix
-// 4) apply labels
-// 5) apply annotations
-// 6) update name reference
+// 1) apply overlay
+// 2) name prefix
+// 3) apply labels
+// 4) apply annotations
+// 5) update name reference
 func (a *applicationImpl) getTransformer(patches types.ResourceCollection) (transformers.Transformer, error) {
 	ts := []transformers.Transformer{}
 
-	nht := transformers.NewNameHashTransformer()
-	ts = append(ts, nht)
-
 	ot, err := transformers.NewOverlayTransformer(types.KObject(patches))
 	if err != nil {
 		return nil, err
diff --git a/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.diff b/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.diff
index 9b5b81f27..c5715182d 100644
--- a/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.diff
+++ b/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.diff
@@ -26,7 +26,7 @@ diff -u -N /tmp/noop/apps_v1beta2_Deployment_nginx.yaml /tmp/transformed/apps_v1
          org: example.com
          team: foo
      spec:
-@@ -30,5 +33,6 @@
+@@ -30,8 +33,12 @@
          - mountPath: /tmp/ps
            name: nginx-persistent-storage
        volumes:
@@ -34,6 +34,37 @@ diff -u -N /tmp/noop/apps_v1beta2_Deployment_nginx.yaml /tmp/transformed/apps_v1
 +      - gcePersistentDisk:
 +          pdName: nginx-persistent-storage
          name: nginx-persistent-storage
+       - configMap:
++          name: staging-configmap-in-overlay-h4hbb8fckf
++        name: configmap-in-overlay
++      - configMap:
+           name: team-foo-configmap-in-base-72t84tc949
+         name: configmap-in-base
+diff -u -N /tmp/noop/v1_ConfigMap_configmap-in-base.yaml /tmp/transformed/v1_ConfigMap_configmap-in-base.yaml
+--- /tmp/noop/v1_ConfigMap_configmap-in-base.yaml	YYYY-MM-DD HH:MM:SS
++++ /tmp/transformed/v1_ConfigMap_configmap-in-base.yaml	YYYY-MM-DD HH:MM:SS
+@@ -8,6 +8,7 @@
+   creationTimestamp: null
+   labels:
+     app: mynginx
++    env: staging
+     org: example.com
+     team: foo
+-  name: team-foo-configmap-in-base-72t84tc949
++  name: staging-team-foo-configmap-in-base-72t84tc949
+diff -u -N /tmp/noop/v1_ConfigMap_configmap-in-overlay.yaml /tmp/transformed/v1_ConfigMap_configmap-in-overlay.yaml
+--- /tmp/noop/v1_ConfigMap_configmap-in-overlay.yaml	YYYY-MM-DD HH:MM:SS
++++ /tmp/transformed/v1_ConfigMap_configmap-in-overlay.yaml	YYYY-MM-DD HH:MM:SS
+@@ -0,0 +1,9 @@
++apiVersion: v1
++data:
++  hello: world
++kind: ConfigMap
++metadata:
++  creationTimestamp: null
++  labels:
++    env: staging
++  name: staging-configmap-in-overlay-h4hbb8fckf
 diff -u -N /tmp/noop/v1_Service_nginx.yaml /tmp/transformed/v1_Service_nginx.yaml
 --- /tmp/noop/v1_Service_nginx.yaml	YYYY-MM-DD HH:MM:SS
 +++ /tmp/transformed/v1_Service_nginx.yaml	YYYY-MM-DD HH:MM:SS
diff --git a/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.yaml b/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.yaml
index d32210902..145a05a66 100644
--- a/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.yaml
+++ b/pkg/kinflate/commands/testdata/testcase-single-overlay/expected.yaml
@@ -1,4 +1,29 @@
 apiVersion: v1
+data:
+  foo: bar
+kind: ConfigMap
+metadata:
+  annotations:
+    note: This is a test annotation
+  creationTimestamp: null
+  labels:
+    app: mynginx
+    env: staging
+    org: example.com
+    team: foo
+  name: staging-team-foo-configmap-in-base-72t84tc949
+---
+apiVersion: v1
+data:
+  hello: world
+kind: ConfigMap
+metadata:
+  creationTimestamp: null
+  labels:
+    env: staging
+  name: staging-configmap-in-overlay-h4hbb8fckf
+---
+apiVersion: v1
 kind: Service
 metadata:
   annotations:
@@ -56,3 +81,9 @@ spec:
       - gcePersistentDisk:
           pdName: nginx-persistent-storage
         name: nginx-persistent-storage
+      - configMap:
+          name: staging-configmap-in-overlay-h4hbb8fckf
+        name: configmap-in-overlay
+      - configMap:
+          name: team-foo-configmap-in-base-72t84tc949
+        name: configmap-in-base
diff --git a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/Kube-manifest.yaml b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/Kube-manifest.yaml
index fcaebd1c7..2ec6d0a6a 100644
--- a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/Kube-manifest.yaml
+++ b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/Kube-manifest.yaml
@@ -10,3 +10,7 @@ patches:
   - deployment.yaml
 packages:
   - ../package/
+configmaps:
+  - name: configmap-in-overlay
+    literals:
+      - hello=world
diff --git a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/deployment.yaml b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/deployment.yaml
index 71316f174..ae8bc1280 100644
--- a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/deployment.yaml
+++ b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/overlay/deployment.yaml
@@ -10,3 +10,6 @@ spec:
         emptyDir: null
         gcePersistentDisk:
           pdName: nginx-persistent-storage
+      - configMap:
+          name: configmap-in-overlay
+        name: configmap-in-overlay
diff --git a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/Kube-manifest.yaml b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/Kube-manifest.yaml
index 9f35bbacd..60ea5ec0a 100644
--- a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/Kube-manifest.yaml
+++ b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/Kube-manifest.yaml
@@ -13,3 +13,7 @@ objectAnnotations:
 resources:
   - deployment.yaml
   - service.yaml
+configmaps:
+  - name: configmap-in-base
+    literals:
+      - foo=bar
diff --git a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/deployment.yaml b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/deployment.yaml
index c998249c3..9f7d3cbb6 100644
--- a/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/deployment.yaml
+++ b/pkg/kinflate/commands/testdata/testcase-single-overlay/in/package/deployment.yaml
@@ -18,4 +18,7 @@ spec:
           mountPath: /tmp/ps
       volumes:
       - name: nginx-persistent-storage
-        emptyDir: {}
\ No newline at end of file
+        emptyDir: {}
+      - configMap:
+          name: configmap-in-base
+        name: configmap-in-base