diff --git a/lib/resourcemerge/core.go b/lib/resourcemerge/core.go
index f8bec5583..950bbe67a 100644
--- a/lib/resourcemerge/core.go
+++ b/lib/resourcemerge/core.go
@@ -24,38 +24,8 @@ func ensurePodTemplateSpec(modified *bool, existing *corev1.PodTemplateSpec, req
 }
 
 func ensurePodSpec(modified *bool, existing *corev1.PodSpec, required corev1.PodSpec) {
-	// any container we specify, we require.
-	for _, required := range required.InitContainers {
-		var existingCurr *corev1.Container
-		for j, curr := range existing.InitContainers {
-			if curr.Name == required.Name {
-				existingCurr = &existing.InitContainers[j]
-				break
-			}
-		}
-		if existingCurr == nil {
-			*modified = true
-			existing.Containers = append(existing.InitContainers, corev1.Container{})
-			existingCurr = &existing.InitContainers[len(existing.InitContainers)-1]
-		}
-		ensureContainer(modified, existingCurr, required)
-	}
-
-	for _, required := range required.Containers {
-		var existingCurr *corev1.Container
-		for j, curr := range existing.Containers {
-			if curr.Name == required.Name {
-				existingCurr = &existing.Containers[j]
-				break
-			}
-		}
-		if existingCurr == nil {
-			*modified = true
-			existing.Containers = append(existing.Containers, corev1.Container{})
-			existingCurr = &existing.Containers[len(existing.Containers)-1]
-		}
-		ensureContainer(modified, existingCurr, required)
-	}
+	ensureContainers(modified, &existing.InitContainers, required.InitContainers)
+	ensureContainers(modified, &existing.Containers, required.Containers)
 
 	// any volume we specify, we require.
 	for _, required := range required.Volumes {
@@ -91,6 +61,37 @@ func ensurePodSpec(modified *bool, existing *corev1.PodSpec, required corev1.Pod
 	setInt32Ptr(modified, &existing.Priority, required.Priority)
 }
 
+func ensureContainers(modified *bool, existing *[]corev1.Container, required []corev1.Container) {
+	var existingCurr *corev1.Container
+	for i, existingContainer := range *existing {
+		for _, requiredContainer := range required {
+			if existingContainer.Name == requiredContainer.Name {
+				existingCurr = &(*existing)[i]
+				ensureContainer(modified, existingCurr, requiredContainer)
+				break
+			}
+		}
+		if existingCurr == nil {
+			*modified = true
+			*existing = append((*existing)[:i], (*existing)[i+1:]...)
+		}
+	}
+
+	for _, requiredContainer := range required {
+		match := false
+		for _, existingContainer := range *existing {
+			if existingContainer.Name == requiredContainer.Name {
+				match = true
+				break
+			}
+		}
+		if !match {
+			*modified = true
+			*existing = append(*existing, requiredContainer)
+		}
+	}
+}
+
 func ensureContainer(modified *bool, existing *corev1.Container, required corev1.Container) {
 	setStringIfSet(modified, &existing.Name, required.Name)
 	setStringIfSet(modified, &existing.Image, required.Image)
diff --git a/lib/resourcemerge/core_test.go b/lib/resourcemerge/core_test.go
index f5f1fc1e0..918400552 100644
--- a/lib/resourcemerge/core_test.go
+++ b/lib/resourcemerge/core_test.go
@@ -5,6 +5,7 @@ import (
 
 	corev1 "k8s.io/api/core/v1"
 	"k8s.io/apimachinery/pkg/api/equality"
+	"k8s.io/apimachinery/pkg/util/diff"
 	"k8s.io/utils/pointer"
 )
 
@@ -16,14 +17,98 @@ func TestEnsurePodSpec(t *testing.T) {
 
 		expectedModified bool
 		expected         corev1.PodSpec
-	}{{
-		name:     "empty inputs",
-		existing: corev1.PodSpec{},
-		input:    corev1.PodSpec{},
+	}{
+		{
+			name:     "empty inputs",
+			existing: corev1.PodSpec{},
+			input:    corev1.PodSpec{},
 
-		expectedModified: false,
-		expected:         corev1.PodSpec{},
-	}}
+			expectedModified: false,
+			expected:         corev1.PodSpec{},
+		},
+		{
+			name: "remove regular containers from existing",
+			existing: corev1.PodSpec{
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test"}}},
+			input: corev1.PodSpec{},
+
+			expectedModified: true,
+			expected:         corev1.PodSpec{},
+		},
+		{
+			name: "remove regular and init containers from existing",
+			existing: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init"}},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test"}}},
+			input: corev1.PodSpec{},
+
+			expectedModified: true,
+			expected:         corev1.PodSpec{},
+		},
+		{
+			name: "remove init containers from existing",
+			existing: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init"}}},
+			input: corev1.PodSpec{},
+
+			expectedModified: true,
+			expected:         corev1.PodSpec{},
+		},
+		{
+			name: "append regular and init containers",
+			existing: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init-a"}},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test-a"}}},
+			input: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init-a"},
+					corev1.Container{Name: "test-init-b"},
+				},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test-a"},
+					corev1.Container{Name: "test-b"},
+				},
+			},
+
+			expectedModified: true,
+			expected: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init-a"},
+					corev1.Container{Name: "test-init-b"},
+				},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test-a"},
+					corev1.Container{Name: "test-b"},
+				},
+			},
+		},
+		{
+			name: "match regular and init containers",
+			existing: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init"}},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test"}}},
+			input: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init"}},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test"}}},
+
+			expectedModified: false,
+			expected: corev1.PodSpec{
+				InitContainers: []corev1.Container{
+					corev1.Container{Name: "test-init"}},
+				Containers: []corev1.Container{
+					corev1.Container{Name: "test"}}},
+		},
+	}
 
 	for _, test := range tests {
 		t.Run(test.name, func(t *testing.T) {
@@ -34,7 +119,7 @@ func TestEnsurePodSpec(t *testing.T) {
 			}
 
 			if !equality.Semantic.DeepEqual(test.existing, test.expected) {
-				t.Errorf("mismatch PodSpec got: %v want: %v", test.existing, test.expected)
+				t.Errorf("unexpected: %s", diff.ObjectReflectDiff(test.expected, test.existing))
 			}
 		})
 	}