diff --git a/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc.go b/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc.go
index d73b587eb0..233d146c13 100644
--- a/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc.go
+++ b/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc.go
@@ -282,3 +282,36 @@ func deleteResources(ctx context.Context, lp sdk.StageLogPersister, applier *pro
 
 	return deletedCount
 }
+
+// findOrphanedKeys returns the keys of resources present in targetManifests
+// but absent from runningManifests.
+func findOrphanedKeys(runningManifests, targetManifests []provider.Manifest) []provider.ResourceKey {
+	runningKeys := make(map[provider.ResourceKey]struct{}, len(runningManifests))
+	for _, m := range runningManifests {
+		runningKeys[m.Key()] = struct{}{}
+	}
+
+	orphans := make([]provider.ResourceKey, 0)
+	for _, m := range targetManifests {
+		if _, exists := runningKeys[m.Key()]; !exists {
+			orphans = append(orphans, m.Key())
+		}
+	}
+	return orphans
+}
+
+// pruneOrphanedResources deletes resources that exist in targetManifests but not in runningManifests.
+// This handles the case where a new resource was applied during the failed deployment and must be
+// removed during rollback to restore the cluster to the last known good state.
+func pruneOrphanedResources(ctx context.Context, lp sdk.StageLogPersister, applier *provider.Applier, runningManifests, targetManifests []provider.Manifest) {
+	orphans := findOrphanedKeys(runningManifests, targetManifests)
+
+	if len(orphans) == 0 {
+		lp.Info("No orphaned resources to prune")
+		return
+	}
+
+	lp.Infof("Found %d orphaned resource(s) to prune", len(orphans))
+	deleted := deleteResources(ctx, lp, applier, orphans)
+	lp.Successf("Successfully pruned %d orphaned resource(s)", deleted)
+}
diff --git a/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc_test.go b/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc_test.go
index c175608730..40b9d64ff8 100644
--- a/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc_test.go
+++ b/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/misc_test.go
@@ -23,6 +23,159 @@ import (
 	"github.com/pipe-cd/pipecd/pkg/app/pipedv1/plugin/kubernetes_multicluster/provider"
 )
 
+func TestFindOrphanedKeys(t *testing.T) {
+	t.Parallel()
+
+	tests := []struct {
+		name             string
+		runningManifests string
+		targetManifests  string
+		wantCount        int
+		wantNames        []string
+	}{
+		{
+			name: "no orphans when target equals running",
+			runningManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+`,
+			targetManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+`,
+			wantCount: 0,
+			wantNames: []string{},
+		},
+		{
+			name:             "all target resources are orphaned when running is empty",
+			runningManifests: "",
+			targetManifests: `
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: new-config
+  namespace: default
+`,
+			wantCount: 1,
+			wantNames: []string{"new-config"},
+		},
+		{
+			name: "new resource in target not present in running is orphaned",
+			runningManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+`,
+			targetManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: new-config
+  namespace: default
+`,
+			wantCount: 1,
+			wantNames: []string{"new-config"},
+		},
+		{
+			name: "resource only in running is not pruned",
+			runningManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: old-config
+  namespace: default
+`,
+			targetManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+`,
+			wantCount: 0,
+			wantNames: []string{},
+		},
+		{
+			name: "multiple orphaned resources",
+			runningManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+`,
+			targetManifests: `
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: app
+  namespace: default
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: new-config
+  namespace: default
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: new-svc
+  namespace: default
+`,
+			wantCount: 2,
+			wantNames: []string{"new-config", "new-svc"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+
+			var running []provider.Manifest
+			if tt.runningManifests != "" {
+				running = mustParseManifests(t, tt.runningManifests)
+			}
+			var target []provider.Manifest
+			if tt.targetManifests != "" {
+				target = mustParseManifests(t, tt.targetManifests)
+			}
+
+			orphans := findOrphanedKeys(running, target)
+
+			assert.Len(t, orphans, tt.wantCount)
+
+			gotNames := make([]string, 0, len(orphans))
+			for _, k := range orphans {
+				gotNames = append(gotNames, k.Name())
+			}
+			for _, name := range tt.wantNames {
+				assert.Contains(t, gotNames, name)
+			}
+		})
+	}
+}
+
 func TestCheckVariantSelectorInWorkload(t *testing.T) {
 	t.Parallel()
 
diff --git a/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/rollback.go b/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/rollback.go
index 9fc8f4c222..c681f97ec2 100644
--- a/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/rollback.go
+++ b/pkg/app/pipedv1/plugin/kubernetes_multicluster/deployment/rollback.go
@@ -210,8 +210,18 @@ func (p *Plugin) rollback(ctx context.Context, input *sdk.ExecuteStageInput[kube
 		failed = true
 	}
 
-	// TODO: prune resources which don't exist in the running manifests but exist in the target manifests.
-	// This occurs when the user adds a new resource and the deployment pipeline fails.
+	lp.Info("Start pruning resources that do not exist in the running manifests")
+	targetCfg, err := input.Request.TargetDeploymentSource.AppConfig()
+	if err != nil {
+		lp.Infof("Failed to load target app config for pruning, skipping: %v", err)
+	} else {
+		targetManifests, err := p.loadManifests(ctx, &input.Request.Deployment, targetCfg.Spec, &input.Request.TargetDeploymentSource, provider.NewLoader(toolRegistry), input.Logger, multiTarget)
+		if err != nil {
+			lp.Infof("Failed to load target manifests for pruning, skipping: %v", err)
+		} else {
+			pruneOrphanedResources(ctx, lp, applier, manifests, targetManifests)
+		}
+	}
 
 	if failed {
 		return sdk.StageStatusFailure