diff --git a/cmd/deploy.go b/cmd/deploy.go
index b8b225d..c866cb9 100644
--- a/cmd/deploy.go
+++ b/cmd/deploy.go
@@ -32,6 +32,7 @@ Examples:
 	cmd.Flags().BoolVar(&helm, "helm", false, "Deploy using Helm charts instead of operator")
 	cmd.Flags().BoolVar(&olm, "olm", false, "Deploy operator via OLM (requires OLM installed)")
 	cmd.Flags().BoolVar(&portForwarding, "port-forwarding", false, "Enable localhost port-forward for Central")
+	cmd.Flags().BoolVar(&pauseReconciliation, "pause-reconciliation", false, "Pause reconciliation after deployment")
 	cmd.Flags().StringVar(&overrideFile, "override", "", "Path to YAML file with overrides")
 	cmd.Flags().StringArrayVar(&overrideSetExpressions, "set", []string{}, "Set override values (can specify multiple times, e.g., --set foo.bar=val)")
 	cmd.Flags().StringVar(&exposure, "exposure", "loadbalancer", "Central exposure backend (loadbalancer, none)")
@@ -125,6 +126,7 @@ func runDeploy(cmd *cobra.Command, args []string) error {
 	d.SetVerbose(verbose)
 	d.SetEarlyReadiness(earlyReadiness)
 	d.SetPortForwardingEnabled(portForwardEnabledFinal)
+	d.SetPauseReconciliation(pauseReconciliation)
 
 	// Resolve "auto" resources based on cluster type
 	resolvedResources := resources
diff --git a/cmd/main.go b/cmd/main.go
index 23c976b..7c96185 100644
--- a/cmd/main.go
+++ b/cmd/main.go
@@ -14,6 +14,7 @@ var (
 	helm                   bool
 	olm                    bool
 	portForwarding         bool
+	pauseReconciliation    bool
 	overrideFile           string
 	overrideSetExpressions []string
 	exposure               string
diff --git a/internal/deployer/deploy_via_operator.go b/internal/deployer/deploy_via_operator.go
index 4b55849..abe953a 100644
--- a/internal/deployer/deploy_via_operator.go
+++ b/internal/deployer/deploy_via_operator.go
@@ -105,6 +105,10 @@ func (d *Deployer) deployCentralOperator(ctx context.Context, resources, exposur
 		return fmt.Errorf("failed waiting for Central: %w", err)
 	}
 
+	if err := d.maybeAddPauseReconcileAnnotation(ctx, "central", "stackrox-central-services", d.centralNamespace); err != nil {
+		d.logger.Warningf("failed to add pause-reconcile annotation: %v", err)
+	}
+
 	return d.configureCentralEndpoint(ctx, exposure)
 }
 
@@ -589,6 +593,10 @@ func (d *Deployer) deploySecuredClusterOperator(ctx context.Context, resources s
 		return fmt.Errorf("failed waiting for SecuredCluster: %w", err)
 	}
 
+	if err := d.maybeAddPauseReconcileAnnotation(ctx, "securedcluster", "stackrox-secured-cluster-services", d.sensorNamespace); err != nil {
+		d.logger.Warningf("failed to add pause-reconcile annotation: %v", err)
+	}
+
 	d.logger.Successf("✓ SecuredCluster '%s' is ready", clusterName)
 	return nil
 }
diff --git a/internal/deployer/deployer.go b/internal/deployer/deployer.go
index 788b327..e64cf4e 100644
--- a/internal/deployer/deployer.go
+++ b/internal/deployer/deployer.go
@@ -25,6 +25,8 @@ var (
 	centralNamespace = "acs-central"
 	sensorNamespace  = "acs-sensor"
 	defaultExposure  = "loadbalancer"
+
+	pauseReconcileAnnotationKey = "stackrox.io/pause-reconcile"
 )
 
 // Deployer is the base deployer for ACS
@@ -46,6 +48,7 @@ type Deployer struct {
 	roxCACertFile          string
 	kubeContext            string
 	portForwardEnabled     bool
+	pauseReconciliation    bool
 	exposure               string
 	overrideFile           string
 	overrideSetExpressions []string
@@ -260,6 +263,9 @@ func (d *Deployer) teardownCentral(ctx context.Context) error {
 
 	d.portForward.Stop()
 
+	// Remove pause-reconcile annotation before deleting to allow operator to clean up properly
+	d.removePauseReconcileAnnotation(ctx, "central", "stackrox-central-services", d.centralNamespace)
+
 	d.logger.Info("Deleting Central custom resource")
 	d.runKubectl(ctx, KubectlOptions{
 		Args:         []string{"delete", "central", "stackrox-central-services", "-n", d.centralNamespace, "--wait=false"},
@@ -292,6 +298,9 @@ func (d *Deployer) teardownSecuredCluster(ctx context.Context) error {
 		return nil
 	}
 
+	// Remove pause-reconcile annotation before deleting to allow operator to clean up properly
+	d.removePauseReconcileAnnotation(ctx, "securedcluster", "stackrox-secured-cluster-services", d.sensorNamespace)
+
 	d.logger.Info("Deleting SecuredCluster custom resource")
 	d.runKubectl(ctx, KubectlOptions{
 		Args:         []string{"delete", "securedcluster", "stackrox-secured-cluster-services", "-n", d.sensorNamespace, "--wait=false"},
@@ -500,6 +509,50 @@ func (d *Deployer) SetEarlyReadiness(enabled bool) {
 	d.earlyReadiness = enabled
 }
 
+func (d *Deployer) SetPauseReconciliation(enabled bool) {
+	d.pauseReconciliation = enabled
+}
+
+// maybeAddPauseReconcileAnnotation adds the stackrox.io/pause-reconcile annotation to a custom resource
+func (d *Deployer) maybeAddPauseReconcileAnnotation(ctx context.Context, resourceType, resourceName, namespace string) error {
+	if !d.pauseReconciliation {
+		return nil
+	}
+
+	d.logger.Infof("Adding pause-reconcile annotation to %s/%s", resourceType, resourceName)
+
+	_, err := d.runKubectl(ctx, KubectlOptions{
+		Args: []string{
+			"annotate", resourceType, resourceName,
+			"-n", namespace,
+			pauseReconcileAnnotationKey,
+			"--overwrite",
+		},
+	})
+	if err != nil {
+		return fmt.Errorf("failed to add pause-reconcile annotation: %w", err)
+	}
+
+	d.logger.Successf("✓ Added pause-reconcile annotation to %s/%s", resourceType, resourceName)
+	return nil
+}
+
+// removePauseReconcileAnnotation removes the stackrox.io/pause-reconcile annotation from a custom resource
+func (d *Deployer) removePauseReconcileAnnotation(ctx context.Context, resourceType, resourceName, namespace string) {
+	d.logger.Dimf("Removing pause-reconcile annotation from %s/%s", resourceType, resourceName)
+
+	_, err := d.runKubectl(ctx, KubectlOptions{
+		Args: []string{
+			"annotate", resourceType, resourceName,
+			"-n", namespace,
+			fmt.Sprintf("%s-", pauseReconcileAnnotationKey),
+		},
+	})
+	if err != nil {
+		d.logger.Dimf("Could not remove pause-reconcile annotation (expected if CR does not exist): %v", err)
+	}
+}
+
 func (d *Deployer) GetDeploymentInfo() (endpoint, password, caCertFile, kubeContext, exposure string) {
 	return d.centralEndpoint, d.centralPassword, d.roxCACertFile, d.kubeContext, d.exposure
 }
diff --git a/tests/e2e/e2e_test.go b/tests/e2e/e2e_test.go
index d4291f7..9a365a2 100644
--- a/tests/e2e/e2e_test.go
+++ b/tests/e2e/e2e_test.go
@@ -6,6 +6,7 @@ package e2e
 import (
 	"bytes"
 	"context"
+	"encoding/json"
 	"fmt"
 	"os"
 	"os/exec"
@@ -296,7 +297,8 @@ func TestDeployBothComponentsTogether(t *testing.T) {
 	defer os.Remove(envrcPath)
 
 	t.Log("=== Deploying both components ===")
-	args := append([]string{roxieBinary, "deploy", "both", "--envrc", envrcPath}, commonDeployArgsNoPortForward...)
+	// We also test --pause-reconciliation flag here.
+	args := append([]string{roxieBinary, "deploy", "both", "--early-readiness", "--pause-reconciliation", "--envrc", envrcPath}, commonDeployArgsNoPortForward...)
 	runCommand(t, deployTimeout*2, nil, args...)
 
 	t.Log("Verifying namespace: acs-central")
@@ -304,6 +306,15 @@ func TestDeployBothComponentsTogether(t *testing.T) {
 
 	t.Log("Verifying namespace: acs-sensor")
 	verifyNamespaceExists(t, "acs-sensor")
+
+	// Verify Central has the pause-reconcile annotation.
+	t.Log("Verifying pause-reconcile annotation on Central CR")
+	verifyAnnotation(t, "central", "stackrox-central-services", "acs-central", "stackrox.io/pause-reconcile", "true")
+
+	// Verify SecuredCluster has the pause-reconcile annotation.
+	t.Log("Verifying pause-reconcile annotation on SecuredCluster CR")
+	verifyAnnotation(t, "securedcluster", "stackrox-secured-cluster-services", "acs-sensor", "stackrox.io/pause-reconcile", "true")
+
 }
 
 func TestDeployCentralAndSecuredClusterViaHelm(t *testing.T) {
@@ -337,3 +348,26 @@ func TestDeployCentralAndSecuredClusterViaHelm(t *testing.T) {
 	t.Log("Verifying namespace: acs-sensor")
 	verifyNamespaceExists(t, "acs-sensor")
 }
+
+func verifyAnnotation(t *testing.T, resourceType, resourceName, namespace, annotationKey, expectedValue string) {
+	t.Helper()
+
+	cmd := exec.Command("kubectl", "get", resourceType, resourceName, "-n", namespace, "-o", "jsonpath={.metadata.annotations}")
+	output, err := cmd.Output()
+	if err != nil {
+		t.Fatalf("Failed to get annotation %s on %s/%s in namespace %s: %v", annotationKey, resourceType, resourceName, namespace, err)
+	}
+
+	annotations := make(map[string]string)
+	err = json.Unmarshal(output, &annotations)
+	if err != nil {
+		t.Fatalf("Failed to unmarshal JSON: %v", err)
+	}
+
+	currentValue := annotations[annotationKey]
+	if currentValue != expectedValue {
+		t.Fatalf("Annotation %s on %s/%s has incorrect value. Expected: %s, Got: %s", annotationKey, resourceType, resourceName, expectedValue, currentValue)
+	}
+
+	t.Logf("✓ Annotation %s=%s verified on %s/%s", annotationKey, expectedValue, resourceType, resourceName)
+}