diff --git a/pkg/canary/config_tracker.go b/pkg/canary/config_tracker.go
index 23e80feb..fafc5af9 100644
--- a/pkg/canary/config_tracker.go
+++ b/pkg/canary/config_tracker.go
@@ -438,5 +438,29 @@ func (ct *ConfigTracker) ApplyPrimaryConfigs(spec corev1.PodSpec, refs map[strin
 		}
 	}
 
+	// update affinity
+	if affinity := spec.Affinity; affinity != nil {
+		if podAntiAffinity := affinity.PodAntiAffinity; podAntiAffinity != nil {
+			for _, preferredAntiAffinity := range podAntiAffinity.PreferredDuringSchedulingIgnoredDuringExecution {
+				term := preferredAntiAffinity.PodAffinityTerm
+				appendPrimarySuffixToValuesIfNeeded(term.TopologyKey, term.LabelSelector)
+			}
+
+			for _, requiredAntiAffinity := range podAntiAffinity.RequiredDuringSchedulingIgnoredDuringExecution {
+				appendPrimarySuffixToValuesIfNeeded(requiredAntiAffinity.TopologyKey, requiredAntiAffinity.LabelSelector)
+			}
+		}
+	}
+
 	return spec
 }
+
+func appendPrimarySuffixToValuesIfNeeded(topologyKey string, labelSelector *metav1.LabelSelector) {
+	if labelSelector != nil && topologyKey == "failure-domain.beta.kubernetes.io/zone" {
+		for _, matchExpression := range labelSelector.MatchExpressions {
+			for i := range matchExpression.Values {
+				matchExpression.Values[i] += "-primary"
+			}
+		}
+	}
+}
diff --git a/pkg/canary/config_tracker_test.go b/pkg/canary/config_tracker_test.go
index 3399db95..d30ea1b0 100644
--- a/pkg/canary/config_tracker_test.go
+++ b/pkg/canary/config_tracker_test.go
@@ -39,6 +39,23 @@ func TestConfigIsDisabled(t *testing.T) {
 	}
 }
 
+func TestConfigTracker_AntiAffinity(t *testing.T) {
+	t.Run("deployment", func(t *testing.T) {
+		dc := deploymentConfigs{name: "podinfo", label: "name", labelValue: "podinfo"}
+		mocks := newDeploymentFixture(dc)
+		mocks.initializeCanary(t)
+
+		depPrimary, err := mocks.kubeClient.AppsV1().Deployments("default").Get(context.TODO(), "podinfo-primary", metav1.GetOptions{})
+		require.NoError(t, err)
+
+		value := depPrimary.Spec.Template.Spec.Affinity.PodAntiAffinity.PreferredDuringSchedulingIgnoredDuringExecution[0].PodAffinityTerm.LabelSelector.MatchExpressions[0].Values[0]
+		assert.Equal(t, "podinfo-primary", value)
+
+		value = depPrimary.Spec.Template.Spec.Affinity.PodAntiAffinity.RequiredDuringSchedulingIgnoredDuringExecution[0].LabelSelector.MatchExpressions[0].Values[0]
+		assert.Equal(t, "podinfo-primary", value)
+	})
+}
+
 func TestConfigTracker_ConfigMaps(t *testing.T) {
 	t.Run("deployment", func(t *testing.T) {
 		dc := deploymentConfigs{name: "podinfo", label: "name", labelValue: "podinfo"}
diff --git a/pkg/canary/deployment_fixture_test.go b/pkg/canary/deployment_fixture_test.go
index da423fd7..997e5c1f 100644
--- a/pkg/canary/deployment_fixture_test.go
+++ b/pkg/canary/deployment_fixture_test.go
@@ -556,6 +556,36 @@ func newDeploymentControllerTest(dc deploymentConfigs) *appsv1.Deployment {
 							},
 						},
 					},
+					Affinity: &corev1.Affinity{
+						PodAntiAffinity: &corev1.PodAntiAffinity{
+							PreferredDuringSchedulingIgnoredDuringExecution: []corev1.WeightedPodAffinityTerm{
+								{
+									PodAffinityTerm: corev1.PodAffinityTerm{
+										TopologyKey: "failure-domain.beta.kubernetes.io/zone",
+										LabelSelector: &metav1.LabelSelector{
+											MatchExpressions: []metav1.LabelSelectorRequirement{
+												{
+													Values: []string{"podinfo"},
+												},
+											},
+										},
+									},
+								},
+							},
+							RequiredDuringSchedulingIgnoredDuringExecution: []corev1.PodAffinityTerm{
+								{
+									TopologyKey: "failure-domain.beta.kubernetes.io/zone",
+									LabelSelector: &metav1.LabelSelector{
+										MatchExpressions: []metav1.LabelSelectorRequirement{
+											{
+												Values: []string{"podinfo"},
+											},
+										},
+									},
+								},
+							},
+						},
+					},
 				},
 			},
 		},