diff --git a/CHANGELOG.md b/CHANGELOG.md
index eb81b1b562..bfb35645aa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,10 +2,16 @@
 
 ### Added
 
+- [PR #476](https://github.com/konpyutaika/nifikop/pull/476) - **[Operator/NifiCluster]** Added logic to include injected containers and init containers in desired pod spec.
+
 ### Changed
 
+- [PR #476](https://github.com/konpyutaika/nifikop/pull/476) - **[Operator/NifiCluster]** Move Zookeeper connectivity check from init container to main container.
+
 ### Fixed Bugs
 
+- [PR #476](https://github.com/konpyutaika/nifikop/pull/476) - **[Operator/NifiCluster]** Fixed istio init race condition and pod reconciliation.
+
 ### Deprecated
 
 ### Removed
diff --git a/pkg/resources/nifi/nifi.go b/pkg/resources/nifi/nifi.go
index 80c821d775..c758c6e280 100644
--- a/pkg/resources/nifi/nifi.go
+++ b/pkg/resources/nifi/nifi.go
@@ -661,6 +661,12 @@ func (r *Reconciler) reconcileNifiPod(log zap.Logger, desiredPod *corev1.Pod) (e
 	}
 
 	if err == nil {
+		// k8s-objectmatcher options
+		opts := []patch.CalculateOption{
+			patch.IgnoreStatusFields(),
+			patch.IgnoreVolumeClaimTemplateTypeMetaAndStatus(),
+			patch.IgnorePDBSelector(),
+		}
 		// Since toleration does not support patchStrategy:"merge,retainKeys", we need to add all toleration from the current pod if the toleration is set in the CR
 		if len(desiredPod.Spec.Tolerations) > 0 {
 			desiredPod.Spec.Tolerations = append(desiredPod.Spec.Tolerations, currentPod.Spec.Tolerations...)
@@ -674,8 +680,55 @@ func (r *Reconciler) reconcileNifiPod(log zap.Logger, desiredPod *corev1.Pod) (e
 			}
 			desiredPod.Spec.Tolerations = uniqueTolerations
 		}
+		// If there are extra initContainers from webhook injections we need to add them
+		if len(currentPod.Spec.InitContainers) > len(desiredPod.Spec.InitContainers) {
+			desiredPod.Spec.InitContainers = append(desiredPod.Spec.InitContainers, currentPod.Spec.InitContainers...)
+			uniqueContainers := []corev1.Container{}
+			keys := make(map[string]bool)
+			for _, c := range desiredPod.Spec.InitContainers {
+				if _, value := keys[c.Name]; !value {
+					keys[c.Name] = true
+					uniqueContainers = append(uniqueContainers, c)
+				}
+			}
+			desiredPod.Spec.InitContainers = uniqueContainers
+		}
+		// If there are extra containers from webhook injections we need to add them
+		if len(currentPod.Spec.Containers) > len(desiredPod.Spec.Containers) {
+			desiredPod.Spec.Containers = append(desiredPod.Spec.Containers, currentPod.Spec.Containers...)
+			uniqueContainers := []corev1.Container{}
+			keys := make(map[string]bool)
+			for _, c := range desiredPod.Spec.Containers {
+				if _, value := keys[c.Name]; !value {
+					keys[c.Name] = true
+					uniqueContainers = append(uniqueContainers, c)
+				}
+			}
+			desiredPod.Spec.Containers = uniqueContainers
+		}
+		// Remove problematic fields if istio
+		if _, ok := currentPod.Annotations["istio.io/rev"]; ok {
+			// Prometheus scrape port is overridden by istio injection
+			delete(currentPod.Annotations, "prometheus.io/port")
+			delete(desiredPod.Annotations, "prometheus.io/port")
+			// Liveness probe port is overridden by istio injection
+			desiredContainer := corev1.Container{}
+			for _, c := range desiredPod.Spec.Containers {
+				if c.Name == "nifi" {
+					desiredContainer = c
+				}
+			}
+			currentContainers := []corev1.Container{}
+			for _, c := range currentPod.Spec.Containers {
+				if c.Name == "nifi" {
+					c.LivenessProbe = desiredContainer.LivenessProbe
+				}
+				currentContainers = append(currentContainers, c)
+			}
+			currentPod.Spec.Containers = currentContainers
+		}
 		// Check if the resource actually updated
-		patchResult, err := patch.DefaultPatchMaker.Calculate(currentPod, desiredPod)
+		patchResult, err := patch.DefaultPatchMaker.Calculate(currentPod, desiredPod, opts...)
 		if err != nil {
 			log.Error("could not match pod objects",
 				zap.String("clusterName", r.NifiCluster.Name),
@@ -697,7 +750,7 @@ func (r *Reconciler) reconcileNifiPod(log zap.Logger, desiredPod *corev1.Pod) (e
 
 				log.Debug("pod resource is in sync",
 					zap.String("clusterName", r.NifiCluster.Name),
-					zap.String("podName", desiredPod.Name))
+					zap.String("podName", currentPod.Name))
 
 				return nil, k8sutil.PodReady(currentPod)
 			}
diff --git a/pkg/resources/nifi/pod.go b/pkg/resources/nifi/pod.go
index 013fcfad02..f341698dfe 100644
--- a/pkg/resources/nifi/pod.go
+++ b/pkg/resources/nifi/pod.go
@@ -95,46 +95,6 @@ func (r *Reconciler) pod(node v1.Node, nodeConfig *v1.NodeConfig, pvcs []corev1.
 	}...)
 
 	podInitContainers := r.injectAdditionalFields(nodeConfig, initContainers)
-	if len(zkAddress) > 0 {
-		podInitContainers = r.injectAdditionalFields(nodeConfig, append(initContainers, []corev1.Container{
-			{
-				Name:            "zookeeper",
-				Image:           r.NifiCluster.Spec.GetInitContainerImage(),
-				ImagePullPolicy: nodeConfig.GetImagePullPolicy(),
-				Env: []corev1.EnvVar{
-					{
-						Name:  "ZK_ADDRESS",
-						Value: zkAddress,
-					},
-				},
-				// The zookeeper init check here just ensures that at least one configured zookeeper host is alive
-				Command: []string{"bash", "-c", `
-set -e
-echo "Trying to contact Zookeeper using connection string: ${ZK_ADDRESS}"
-
-connected=0
-IFS=',' read -r -a zk_hosts <<< "${ZK_ADDRESS}"
-until [ $connected -eq 1 ]
-do
-for zk_host in "${zk_hosts[@]}"
-do
-	IFS=':' read -r -a zk_host_port <<< "${zk_host}"
-	
-	echo "Checking Zookeeper Host: [${zk_host_port[0]}] Port: [${zk_host_port[1]}]"
-	nc -vzw 1 ${zk_host_port[0]} ${zk_host_port[1]}
-	if [ $? -eq 0 ]; then
-		echo "Connected to ${zk_host_port}"
-		connected=1
-	fi
-done
-
-sleep 1
-done
-`},
-				Resources: generateInitContainerResources(),
-			},
-		}...))
-	}
 
 	sort.Slice(podVolumes, func(i, j int) bool {
 		return podVolumes[i].Name < podVolumes[j].Name
@@ -534,12 +494,40 @@ do
 		notMatchedIp=false
 	fi
 done
-echo "Hostname is successfully binded withy IP address"`, nodeAddress, nodeAddress)
+echo "Hostname is successfully binded with IP address"`, nodeAddress, nodeAddress)
+	}
+
+	zkResolve := ""
+	if len(zkAddress) > 0 {
+		zkResolve = `echo "Trying to contact Zookeeper using connection string: ${NIFI_ZOOKEEPER_CONNECT_STRING}"
+
+connected=0
+IFS=',' read -r -a zk_hosts <<< "${NIFI_ZOOKEEPER_CONNECT_STRING}"
+until [ $connected -eq 1 ]
+do
+	for zk_host in "${zk_hosts[@]}"
+	do
+		IFS=':' read -r -a zk_host_port <<< "${zk_host}"
+
+		echo "Checking Zookeeper Host: [${zk_host_port[0]}] Port: [${zk_host_port[1]}]"
+		set +e
+		curl --telnet-option 'BOGUS=1' --connect-timeout 2 -s telnet://${zk_host_port[0]}:${zk_host_port[1]} < /dev/null
+		if [ $? -eq 48 ]; then
+			echo "Connected to ${zk_host_port}"
+			connected=1
+		fi
+		set -e
+	done
+
+	sleep 1
+done`
 	}
+
 	command := []string{"bash", "-ce", fmt.Sprintf(`cp ${NIFI_HOME}/tmp/* ${NIFI_HOME}/conf/
 %s
 %s
-exec bin/nifi.sh run`, resolveIp, singleUser)}
+%s
+exec bin/nifi.sh run`, zkResolve, resolveIp, singleUser)}
 
 	return corev1.Container{
 		Name:            ContainerName,