diff --git a/api/filters/fieldspec/fieldspec.go b/api/filters/fieldspec/fieldspec.go
index 3811afec9..d728e9ebc 100644
--- a/api/filters/fieldspec/fieldspec.go
+++ b/api/filters/fieldspec/fieldspec.go
@@ -64,7 +64,7 @@ func (fltr Filter) filter(obj *yaml.RNode) error {
 		// found the field -- set its value
 		return fltr.SetValue(obj)
 	}
-	if obj.IsTaggedNull() {
+	if obj.IsTaggedNull() || obj.IsNil() {
 		return nil
 	}
 	switch obj.YNode().Kind {
diff --git a/api/internal/target/multitransformer.go b/api/internal/target/multitransformer.go
index 8eccb4956..98d6378d5 100644
--- a/api/internal/target/multitransformer.go
+++ b/api/internal/target/multitransformer.go
@@ -42,6 +42,14 @@ func (o *multiTransformer) transform(m resmap.ResMap) error {
 			return err
 		}
 	}
+	for _, r := range m.Resources() {
+		if r.IsEmpty() {
+			err := m.Remove(r.CurId())
+			if err != nil {
+				return err
+			}
+		}
+	}
 	return nil
 }
 
diff --git a/api/krusty/multiplepatch_test.go b/api/krusty/multiplepatch_test.go
index a093007bc..488c0e437 100644
--- a/api/krusty/multiplepatch_test.go
+++ b/api/krusty/multiplepatch_test.go
@@ -1213,3 +1213,52 @@ spec:
           name: server
 `)
 }
+
+// test for #3616
+func TestSmpDeleteOnResource(t *testing.T) {
+	th := kusttest_test.MakeHarness(t)
+	th.WriteK(".", `
+resources:
+- workloads.yaml
+patches:
+- patch: |
+    apiVersion: monitoring.coreos.com/v1
+    kind: PrometheusRule
+    metadata:
+      name: rule1
+    $patch: delete
+`)
+	th.WriteF("workloads.yaml", `
+apiVersion: monitoring.coreos.com/v1
+kind: PrometheusRule
+metadata:
+  labels:
+    role: alert-rules
+  name: rule1
+spec:
+  groups:
+  - name: rabbitmq.rules
+---
+apiVersion: monitoring.coreos.com/v1
+kind: PrometheusRule
+metadata:
+  labels:
+    role: alert-rules
+  name: rule2
+spec:
+  groups:
+  - name: rabbitmq.rules
+`)
+	m := th.Run(".", th.MakeDefaultOptions())
+	th.AssertActualEqualsExpected(m, `
+apiVersion: monitoring.coreos.com/v1
+kind: PrometheusRule
+metadata:
+  labels:
+    role: alert-rules
+  name: rule2
+spec:
+  groups:
+  - name: rabbitmq.rules
+`)
+}