diff --git a/cmd/antrea-agent/agent.go b/cmd/antrea-agent/agent.go
index 9b0ab2db775..b05eadffca1 100644
--- a/cmd/antrea-agent/agent.go
+++ b/cmd/antrea-agent/agent.go
@@ -294,6 +294,16 @@ func run(o *Options) error {
 		NodePortAddressesIPv6: nodePortAddressesIPv6,
 	}
 
+	if features.DefaultFeatureGate.Enabled(features.SecondaryNetwork) {
+		bridgeConfig := o.config.SecondaryNetwork.OVSBridges[0]
+		ovsSecBridgeClient := ovsconfig.NewOVSBridge(bridgeConfig.BridgeName, ovsDatapathType, ovsdbConnection, ovsconfig.WithRequiredPortExternalIDs(interfacestore.AntreaInterfaceTypeKey))
+		secondaryBridge :=agent.NewSecondaryBridgeInitializer(ovsSecBridgeClient, ifaceStore, bridgeConfig.BridgeName)
+		err := secondaryBridge.InitializeInterfaceStore()
+		if err != nil {
+		  klog.ErrorS(err, "Failed to initialize the secondary bridge interface store")
+		}
+	}
+
 	// Initialize agent and node network.
 	agentInitializer := agent.NewInitializer(
 		k8sClient,
diff --git a/pkg/agent/agent.go b/pkg/agent/agent.go
index 7faa6dd90e2..5294ad4ae9e 100644
--- a/pkg/agent/agent.go
+++ b/pkg/agent/agent.go
@@ -195,6 +195,24 @@ func NewInitializer(
 	}
 }
 
+type SecondaryBridgeInitializer struct {
+    ovsClient     ovsconfig.OVSBridgeClient
+    ifaceStore    interfacestore.InterfaceStore
+    bridgeName    string
+}
+
+func NewSecondaryBridgeInitializer(
+    ovsClient ovsconfig.OVSBridgeClient,
+    ifaceStore interfacestore.InterfaceStore,
+    bridgeName string,
+) *SecondaryBridgeInitializer {
+    return &SecondaryBridgeInitializer{
+        ovsClient:  ovsClient,
+        ifaceStore: ifaceStore,
+        bridgeName: bridgeName,
+    }
+}
+
 // GetNodeConfig returns the NodeConfig.
 func (i *Initializer) GetNodeConfig() *config.NodeConfig {
 	return i.nodeConfig
@@ -274,6 +292,47 @@ func (i *Initializer) validateSupportedDPFeatures() error {
 	return nil
 }
 
+func (s *SecondaryBridgeInitializer) InitializeInterfaceStore() error {
+    ovsPorts, err := s.ovsClient.GetPortList()
+    if err != nil {
+        klog.ErrorS(err, "Failed to list OVS ports for the secondary bridge", "bridgeName", s.bridgeName)
+        return err
+    }
+
+    ifaceList := make([]*interfacestore.InterfaceConfig, 0, len(ovsPorts))
+    for index := range ovsPorts {
+        port := &ovsPorts[index]
+        ovsPort := &interfacestore.OVSPortConfig{
+            PortUUID: port.UUID,
+            OFPort:   port.OFPort,
+        }
+
+        interfaceType, ok := port.ExternalIDs[interfacestore.AntreaInterfaceTypeKey]
+        if !ok {
+            klog.InfoS("Interface type is not set for the secondary bridge", "interfaceName", port.Name)
+            continue
+        }
+
+        var intf *interfacestore.InterfaceConfig
+        switch interfaceType {
+        case interfacestore.AntreaContainer:
+            intf = cniserver.ParseOVSPortInterfaceConfig(port, ovsPort)
+        default:
+            klog.InfoS("Unknown Antrea interface type for the secondary bridge", "type", interfaceType)
+        }
+
+        if intf != nil {
+            ifaceList = append(ifaceList, intf)
+        }
+
+    }
+
+    s.ifaceStore.Initialize(ifaceList)
+    klog.InfoS("Successfully initialized the secondary bridge interface store", "bridgeName", s.bridgeName)
+
+    return nil
+}
+
 // initInterfaceStore initializes InterfaceStore with all OVS ports retrieved
 // from the OVS bridge.
 func (i *Initializer) initInterfaceStore() error {
diff --git a/pkg/agent/cniserver/pod_configuration.go b/pkg/agent/cniserver/pod_configuration.go
index e1ad05752eb..43246340874 100644
--- a/pkg/agent/cniserver/pod_configuration.go
+++ b/pkg/agent/cniserver/pod_configuration.go
@@ -468,7 +468,7 @@ func (pc *podConfigurator) reconcile(pods []corev1.Pod, containerAccess *contain
 				continue
 			}
 			podWg.Add(1)
-			go func(containerID, pod, namespace string) {
+			go func(containerID, iface, pod, namespace string) {
 				defer podWg.Done()
 				// Do not install Pod flows until all preconditions are met.
 				podNetworkWait.Wait()
@@ -476,7 +476,7 @@ func (pc *podConfigurator) reconcile(pods []corev1.Pod, containerAccess *contain
 				containerAccess.lockContainer(containerID)
 				defer containerAccess.unlockContainer(containerID)
 
-				containerConfig, exists := pc.ifaceStore.GetContainerInterface(containerID)
+				containerConfig, exists := pc.ifaceStore.GetInterfaceByName(iface)
 				if !exists {
 					klog.InfoS("The container interface had been deleted, skip installing flows for Pod", "Pod", klog.KRef(namespace, name), "containerID", containerID)
 					return
@@ -496,7 +496,7 @@ func (pc *podConfigurator) reconcile(pods []corev1.Pod, containerAccess *contain
 				); err != nil {
 					klog.ErrorS(err, "Error when re-installing flows for Pod", "Pod", klog.KRef(namespace, name))
 				}
-			}(containerConfig.ContainerID, name, namespace)
+			}(containerConfig.ContainerID, containerConfig.InterfaceName, name, namespace)
 		} else {
 			// clean-up and delete interface
 			klog.V(4).InfoS("Deleting interface", "Pod", klog.KRef(namespace, name), "iface", containerConfig.InterfaceName)