diff --git a/e2e/nomostest/config_sync.go b/e2e/nomostest/config_sync.go
index 58918a7803..cdd4200af6 100644
--- a/e2e/nomostest/config_sync.go
+++ b/e2e/nomostest/config_sync.go
@@ -78,6 +78,16 @@ const (
 	shortSyncPollingPeriod = 5 * time.Second
 )
 
+// InstallMethod defines how Config Sync should be installed
+type InstallMethod string
+
+const (
+	// InstallMethodApply uses server-side apply (default)
+	InstallMethodApply InstallMethod = "apply"
+	// InstallMethodUpdate uses client-side update
+	InstallMethodUpdate InstallMethod = "update"
+)
+
 var (
 	// baseDir is the path to the Nomos repository root from test case files.
 	//
@@ -230,16 +240,36 @@ func parseConfigSyncManifests(nt *NT) ([]client.Object, error) {
 }
 
 // InstallConfigSync installs ConfigSync on the test cluster
-func InstallConfigSync(nt *NT) error {
-	nt.T.Log("[SETUP] Installing Config Sync")
+func InstallConfigSync(nt *NT, method InstallMethod) error {
+	nt.T.Log("[SETUP] Installing Config Sync using method: ", method)
 	objs, err := parseConfigSyncManifests(nt)
 	if err != nil {
 		return err
 	}
 	for _, o := range objs {
 		nt.T.Logf("installConfigSync obj: %v", core.GKNN(o))
-		if err := nt.KubeClient.Apply(o); err != nil {
-			return err
+		switch method {
+		case InstallMethodApply:
+			if err := nt.KubeClient.Apply(o); err != nil {
+				return err
+			}
+		case InstallMethodUpdate:
+			currentObj := o.DeepCopyObject().(client.Object)
+			if err := nt.KubeClient.Get(currentObj.GetName(), currentObj.GetNamespace(), currentObj); err != nil {
+				if apierrors.IsNotFound(err) {
+					if err := nt.KubeClient.Create(o); err != nil {
+						return err
+					}
+				} else {
+					return err
+				}
+			} else {
+				// Attach existing resourceVersion to the object
+				o.SetResourceVersion(currentObj.GetResourceVersion())
+				if err := nt.KubeClient.Update(o); err != nil {
+					return err
+				}
+			}
 		}
 	}
 	return nil
diff --git a/e2e/nomostest/new.go b/e2e/nomostest/new.go
index 316f06b0ca..47d67da80f 100644
--- a/e2e/nomostest/new.go
+++ b/e2e/nomostest/new.go
@@ -385,7 +385,7 @@ func FreshTestEnv(t nomostesting.NTB, opts *ntopts.New) *NT {
 		return setupRegistry(nt)
 	})
 	tg.Go(func() error {
-		return InstallConfigSync(nt)
+		return InstallConfigSync(nt, InstallMethodApply)
 	})
 	tg.Go(func() error {
 		return installPrometheus(nt)
diff --git a/e2e/testcases/cli_test.go b/e2e/testcases/cli_test.go
index 854051e3e5..e19b700825 100644
--- a/e2e/testcases/cli_test.go
+++ b/e2e/testcases/cli_test.go
@@ -1297,13 +1297,14 @@ func TestApiResourceFormatting(t *testing.T) {
 }
 
 func TestNomosMigrate(t *testing.T) {
-	nt := nomostest.New(t, nomostesting.NomosCLI, ntopts.SkipConfigSyncInstall)
+	nt := nomostest.New(t, nomostesting.NomosCLI)
 
 	nt.T.Cleanup(func() {
 		// Restore state of Config Sync installation after test
-		if err := nomostest.InstallConfigSync(nt); err != nil {
+		if err := nomostest.InstallConfigSync(nt, nomostest.InstallMethodUpdate); err != nil {
 			nt.T.Fatal(err)
 		}
+		nt.Must(nt.WatchForAllSyncs())
 	})
 	nt.T.Cleanup(func() {
 		cmObj := &unstructured.Unstructured{
@@ -1451,11 +1452,11 @@ func TestNomosMigrate(t *testing.T) {
 			configmanagement.RGControllerName, configmanagement.RGControllerNamespace)
 	})
 	tg.Go(func() error {
-		return nt.Watcher.WatchForNotFound(kinds.Deployment(),
+		return nt.Watcher.WatchForCurrentStatus(kinds.Deployment(),
 			core.RootReconcilerName(configsync.RootSyncName), configsync.ControllerNamespace)
 	})
 	tg.Go(func() error {
-		return nt.Watcher.WatchForNotFound(kinds.RootSyncV1Beta1(),
+		return nt.Watcher.WatchForCurrentStatus(kinds.RootSyncV1Beta1(),
 			configsync.RootSyncName, configsync.ControllerNamespace)
 	})
 	if err := tg.Wait(); err != nil {
@@ -1464,14 +1465,14 @@ func TestNomosMigrate(t *testing.T) {
 }
 
 func TestNomosMigrateMonoRepo(t *testing.T) {
-	nt := nomostest.New(t, nomostesting.NomosCLI, ntopts.SkipConfigSyncInstall)
+	nt := nomostest.New(t, nomostesting.NomosCLI)
 
 	nt.T.Cleanup(func() {
 		// Restore state of Config Sync installation after test.
-		// This also emulates upgrading to the current version after migrating
-		if err := nomostest.InstallConfigSync(nt); err != nil {
+		if err := nomostest.InstallConfigSync(nt, nomostest.InstallMethodUpdate); err != nil {
 			nt.T.Fatal(err)
 		}
+		nt.Must(nt.WatchForAllSyncs())
 	})
 	nt.T.Cleanup(func() {
 		crds := []string{
@@ -1707,13 +1708,14 @@ func TestNomosMigrateMonoRepo(t *testing.T) {
 // This test case validates the behavior of the uninstall script defined
 // at installation/uninstall_configmanagement.sh
 func TestACMUninstallScript(t *testing.T) {
-	nt := nomostest.New(t, nomostesting.NomosCLI, ntopts.SkipConfigSyncInstall)
+	nt := nomostest.New(t, nomostesting.NomosCLI)
 
 	nt.T.Cleanup(func() {
 		// Restore state of Config Sync installation after test
-		if err := nomostest.InstallConfigSync(nt); err != nil {
+		if err := nomostest.InstallConfigSync(nt, nomostest.InstallMethodUpdate); err != nil {
 			nt.T.Fatal(err)
 		}
+		nt.Must(nt.WatchForAllSyncs())
 	})
 	nt.T.Cleanup(func() {
 		cmObj := &unstructured.Unstructured{
@@ -1861,11 +1863,11 @@ func TestACMUninstallScript(t *testing.T) {
 			configmanagement.RGControllerName, configmanagement.RGControllerNamespace)
 	})
 	tg.Go(func() error {
-		return nt.Watcher.WatchForNotFound(kinds.Deployment(),
+		return nt.Watcher.WatchForCurrentStatus(kinds.Deployment(),
 			core.RootReconcilerName(configsync.RootSyncName), configsync.ControllerNamespace)
 	})
 	tg.Go(func() error {
-		return nt.Watcher.WatchForNotFound(kinds.RootSyncV1Beta1(),
+		return nt.Watcher.WatchForCurrentStatus(kinds.RootSyncV1Beta1(),
 			configsync.RootSyncName, configsync.ControllerNamespace)
 	})
 	if err := tg.Wait(); err != nil {