diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/ApplicationAuthenticator.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/ApplicationAuthenticator.java
index 6c974a31d83b..b78e85aa6f49 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/ApplicationAuthenticator.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/ApplicationAuthenticator.java
@@ -171,4 +171,17 @@ default String getI18nKey() {
         return StringUtils.EMPTY;
     }
 
+    default AuthenticatorType getAuthenticatorType() {
+
+        return AuthenticatorType.SYSTEM;
+    }
+
+    /**
+     * The Authentication Type - SYSTEM: system define authenticator, CUSTOM: user defined authentication extension.
+     */
+    enum AuthenticatorType {
+
+        SYSTEM,
+        CUSTOM
+    }
 }
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandler.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandler.java
index 8a9939ea241d..e073603d863d 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandler.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandler.java
@@ -34,6 +34,7 @@
 import org.wso2.carbon.consent.mgt.core.model.ReceiptPurposeInput;
 import org.wso2.carbon.consent.mgt.core.model.ReceiptServiceInput;
 import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator;
+import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator.AuthenticatorType;
 import org.wso2.carbon.identity.application.authentication.framework.FederatedApplicationAuthenticator;
 import org.wso2.carbon.identity.application.authentication.framework.config.ConfigurationFacade;
 import org.wso2.carbon.identity.application.authentication.framework.config.model.AuthenticatorConfig;
@@ -187,7 +188,11 @@ private PostAuthnHandlerFlowStatus handleResponseFlow(HttpServletRequest request
             AuthenticatorConfig authenticatorConfig = stepConfig.getAuthenticatedAutenticator();
             ApplicationAuthenticator authenticator = authenticatorConfig.getApplicationAuthenticator();
 
-            if (authenticator instanceof FederatedApplicationAuthenticator) {
+            AuthenticatorType authenticatorType = authenticator.getAuthenticatorType();
+            if ((AuthenticatorType.SYSTEM.equals(authenticatorType) && authenticator instanceof
+                    FederatedApplicationAuthenticator) || (AuthenticatorType.CUSTOM.equals(authenticatorType) 
+                    && stepConfig.getAuthenticatedUser().isFederatedUser())) {
+                
                 String externalIdPConfigName = stepConfig.getAuthenticatedIdP();
                 ExternalIdPConfig externalIdPConfig = getExternalIdpConfig(externalIdPConfigName, context);
                 context.setExternalIdP(externalIdPConfig);
@@ -295,7 +300,11 @@ private PostAuthnHandlerFlowStatus handleRequestFlow(HttpServletRequest request,
             }
             ApplicationAuthenticator authenticator = authenticatorConfig.getApplicationAuthenticator();
 
-            if (authenticator instanceof FederatedApplicationAuthenticator) {
+            AuthenticatorType authenticatorType = authenticator.getAuthenticatorType();
+            if ((AuthenticatorType.SYSTEM.equals(authenticatorType) && authenticator instanceof
+                    FederatedApplicationAuthenticator) || (AuthenticatorType.CUSTOM.equals(authenticatorType)
+                    && stepConfig.getAuthenticatedUser().isFederatedUser())) {
+                
                 String externalIdPConfigName = stepConfig.getAuthenticatedIdP();
                 ExternalIdPConfig externalIdPConfig = getExternalIdpConfig(externalIdPConfigName, context);
                 context.setExternalIdP(externalIdPConfig);
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandler.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandler.java
index ce831f298fd2..ff759fcb2392 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandler.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandler.java
@@ -24,6 +24,7 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator;
+import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator.AuthenticatorType;
 import org.wso2.carbon.identity.application.authentication.framework.FederatedApplicationAuthenticator;
 import org.wso2.carbon.identity.application.authentication.framework.config.model.AuthenticatorConfig;
 import org.wso2.carbon.identity.application.authentication.framework.config.model.SequenceConfig;
@@ -114,7 +115,11 @@ public PostAuthnHandlerFlowStatus handle(HttpServletRequest request, HttpServlet
             }
             ApplicationAuthenticator authenticator = authenticatorConfig.getApplicationAuthenticator();
 
-            if (authenticator instanceof FederatedApplicationAuthenticator) {
+           AuthenticatorType authenticatorType = authenticator.getAuthenticatorType();
+            if ((AuthenticatorType.SYSTEM.equals(authenticatorType) && authenticator instanceof
+                    FederatedApplicationAuthenticator) || (AuthenticatorType.CUSTOM.equals(authenticatorType)
+                    && stepConfig.getAuthenticatedUser().isFederatedUser())) {
+
                 if (stepConfig.isSubjectIdentifierStep()) {
                     if (log.isDebugEnabled()) {
                         log.debug(authenticator.getName() + " has been set up for subject identifier step.");
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/sequence/impl/DefaultStepBasedSequenceHandler.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/sequence/impl/DefaultStepBasedSequenceHandler.java
index 3b5b4634cb38..5dc981a0c69a 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/sequence/impl/DefaultStepBasedSequenceHandler.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/sequence/impl/DefaultStepBasedSequenceHandler.java
@@ -24,6 +24,7 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator;
+import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator.AuthenticatorType;
 import org.wso2.carbon.identity.application.authentication.framework.AuthenticationFlowHandler;
 import org.wso2.carbon.identity.application.authentication.framework.FederatedApplicationAuthenticator;
 import org.wso2.carbon.identity.application.authentication.framework.config.ConfigurationFacade;
@@ -289,7 +290,10 @@ protected void handlePostAuthentication(HttpServletRequest request,
 
             stepCount++;
 
-            if (authenticator instanceof FederatedApplicationAuthenticator) {
+            AuthenticatorType authenticatorType = authenticator.getAuthenticatorType();
+            if ((AuthenticatorType.SYSTEM.equals(authenticatorType) && authenticator instanceof
+                    FederatedApplicationAuthenticator) || (AuthenticatorType.CUSTOM.equals(authenticatorType)
+                    && stepConfig.getAuthenticatedUser().isFederatedUser())) {
 
                 ExternalIdPConfig externalIdPConfig = null;
                 try {
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/step/impl/DefaultStepHandler.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/step/impl/DefaultStepHandler.java
index 3633d3c01097..d8ed4e2f4ede 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/step/impl/DefaultStepHandler.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/handler/step/impl/DefaultStepHandler.java
@@ -28,6 +28,7 @@
 import org.wso2.carbon.CarbonConstants;
 import org.wso2.carbon.context.PrivilegedCarbonContext;
 import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator;
+import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator.AuthenticatorType;
 import org.wso2.carbon.identity.application.authentication.framework.AuthenticationFlowHandler;
 import org.wso2.carbon.identity.application.authentication.framework.AuthenticatorFlowStatus;
 import org.wso2.carbon.identity.application.authentication.framework.FederatedApplicationAuthenticator;
@@ -771,7 +772,10 @@ protected void doAuthentication(HttpServletRequest request, HttpServletResponse
                 context.getSubject().setAccessingOrganization(userResidentOrganization);
             }
 
-            if (authenticator instanceof FederatedApplicationAuthenticator) {
+            AuthenticatorType authenticatorType = authenticator.getAuthenticatorType();
+            if ((AuthenticatorType.SYSTEM.equals(authenticatorType) && authenticator instanceof
+                    FederatedApplicationAuthenticator) || (AuthenticatorType.CUSTOM.equals(authenticatorType)
+                    && context.getSubject().isFederatedUser())) {
 
                 if (context.getSubject().getUserName() == null) {
                     // Set subject identifier as the default username for federated users
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/util/FrameworkUtils.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/util/FrameworkUtils.java
index 88c9a095f651..b79c71165b99 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/util/FrameworkUtils.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/main/java/org/wso2/carbon/identity/application/authentication/framework/util/FrameworkUtils.java
@@ -38,6 +38,7 @@
 import org.wso2.carbon.core.util.CryptoException;
 import org.wso2.carbon.core.util.CryptoUtil;
 import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator;
+import org.wso2.carbon.identity.application.authentication.framework.ApplicationAuthenticator.AuthenticatorType;
 import org.wso2.carbon.identity.application.authentication.framework.AuthenticationDataPublisher;
 import org.wso2.carbon.identity.application.authentication.framework.AuthenticationFlowHandler;
 import org.wso2.carbon.identity.application.authentication.framework.AuthenticatorFlowStatus;
@@ -3395,7 +3396,11 @@ public static boolean isJITProvisioningEnabled(AuthenticationContext context)
             }
             ApplicationAuthenticator authenticator = authenticatorConfig.getApplicationAuthenticator();
 
-            if (authenticator instanceof FederatedApplicationAuthenticator) {
+            AuthenticatorType authenticatorType = authenticator.getAuthenticatorType();
+            if ((AuthenticatorType.SYSTEM.equals(authenticatorType) && authenticator instanceof
+                    FederatedApplicationAuthenticator) || (AuthenticatorType.CUSTOM.equals(authenticatorType)
+                    && stepConfig.getAuthenticatedUser().isFederatedUser())) {
+                
                 ExternalIdPConfig externalIdPConfig;
                 String externalIdPConfigName = stepConfig.getAuthenticatedIdP();
                 externalIdPConfig = getExternalIdpConfig(externalIdPConfigName, context);
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandlerTest.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandlerTest.java
index 7fe64ac03758..8264e30cc127 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandlerTest.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/JITProvisioningPostAuthenticationHandlerTest.java
@@ -66,7 +66,6 @@
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.anyString;
-import static org.mockito.Mockito.doReturn;
 import static org.mockito.Mockito.lenient;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.mockStatic;
@@ -165,7 +164,8 @@ public void testHandleWithAuthenticatedUserWithFederatedIdp() throws FrameworkEx
             configurationFacade.when(ConfigurationFacade::getInstance).thenReturn(mockConfigurationFacade);
             IdentityProvider identityProvider = getTestIdentityProvider("default-tp-1.xml");
             ExternalIdPConfig externalIdPConfig = new ExternalIdPConfig(identityProvider);
-            doReturn(externalIdPConfig).when(mockConfigurationFacade).getIdPConfigByName(eq(null), anyString());
+            lenient().doReturn(externalIdPConfig).when(mockConfigurationFacade)
+                    .getIdPConfigByName(eq(null), anyString());
 
             PostAuthnHandlerFlowStatus postAuthnHandlerFlowStatus = postJITProvisioningHandler
                     .handle(request, response, context);
diff --git a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandlerTest.java b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandlerTest.java
index 9c172b60891f..6acc4d4045d9 100644
--- a/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandlerTest.java
+++ b/components/authentication-framework/org.wso2.carbon.identity.application.authentication.framework/src/test/java/org/wso2/carbon/identity/application/authentication/framework/handler/request/impl/PostAuthAssociationHandlerTest.java
@@ -212,6 +212,8 @@ private AuthenticationContext processAndGetAuthenticationContext(ServiceProvider
         if (isFederated) {
             applicationAuthenticator = mock(FederatedApplicationAuthenticator.class);
         }
+        when(applicationAuthenticator.getAuthenticatorType())
+                .thenReturn(ApplicationAuthenticator.AuthenticatorType.SYSTEM);
         when(applicationAuthenticator.getName()).thenReturn("Authenticator1");
 
         if (withAuthenticatedUser) {