diff --git a/components/org.wso2.carbon.identity.governance/src/main/java/org/wso2/carbon/identity/governance/IdentityGovernanceServiceImpl.java b/components/org.wso2.carbon.identity.governance/src/main/java/org/wso2/carbon/identity/governance/IdentityGovernanceServiceImpl.java
index f6a4ae08a..239a2c5cb 100644
--- a/components/org.wso2.carbon.identity.governance/src/main/java/org/wso2/carbon/identity/governance/IdentityGovernanceServiceImpl.java
+++ b/components/org.wso2.carbon.identity.governance/src/main/java/org/wso2/carbon/identity/governance/IdentityGovernanceServiceImpl.java
@@ -42,6 +42,9 @@
 public class IdentityGovernanceServiceImpl implements IdentityGovernanceService {
 
     private static final Log log = LogFactory.getLog(IdentityGovernanceServiceImpl.class);
+    private static final String EMAIL_OTP_AUTHENTICATOR = "email-otp-authenticator";
+    public static final String EMAIL_OTP_USE_ALPHANUMERIC_CHARS = "EmailOTP.OtpRegex.UseAlphanumericChars";
+    public static final String EMAIL_OTP_USE_NUMERIC_CHARS = "EmailOTP.OtpRegex.UseNumericChars";
 
     public void updateConfiguration(String tenantDomain, Map<String, String> configurationDetails)
             throws IdentityGovernanceException {
@@ -52,17 +55,13 @@ public void updateConfiguration(String tenantDomain, Map<String, String> configu
 
             IdentityProviderProperty[] identityMgtProperties = residentIdp.getIdpProperties();
             List<IdentityProviderProperty> newProperties = new ArrayList<>();
+            migratePropertyUseNumericToUseAlphaNumeric(configurationDetails);
             for (IdentityProviderProperty identityMgtProperty : identityMgtProperties) {
                 IdentityProviderProperty prop = new IdentityProviderProperty();
                 String key = identityMgtProperty.getName();
                 prop.setName(key);
                 if (configurationDetails.containsKey(key)) {
                     prop.setValue(configurationDetails.get(key));
-                    if (Objects.equals(key, "EmailOTP.OtpRegex.Migrated")) {
-                        prop.setValue("true");
-                    } else {
-                        prop.setValue(configurationDetails.get(key));
-                    }
                 } else {
                     prop.setValue(identityMgtProperty.getValue());
                 }
@@ -247,6 +246,21 @@ public ConnectorConfig getConnectorWithConfigs(String tenantDomain,
         return null;
     }
 
+    /**
+     * This method is used to make sure property value useNumericCharacters and useAlphanumericCharacters both uses
+     * same user input.
+     *
+     * @param configurationDetails Configuration details of the email OTP connector.
+     */
+    private void migratePropertyUseNumericToUseAlphaNumeric(Map<String, String> configurationDetails) {
+
+        if (configurationDetails.containsKey(EMAIL_OTP_USE_ALPHANUMERIC_CHARS) &&
+                configurationDetails.containsKey(EMAIL_OTP_USE_NUMERIC_CHARS)) {
+            boolean useNumericChars = !Boolean.parseBoolean(configurationDetails.get(EMAIL_OTP_USE_ALPHANUMERIC_CHARS));
+            configurationDetails.put(EMAIL_OTP_USE_NUMERIC_CHARS, String.valueOf(useNumericChars));
+        }
+    }
+
     /**
      * This method is used to migrate the property value useNumericCharacters to useAlphanumericCharacters.
      *
@@ -255,18 +269,20 @@ public ConnectorConfig getConnectorWithConfigs(String tenantDomain,
      */
     private void migratePropertyUseNumericToUseAlphaNumeric(String connectorName, ConnectorConfig connectorConfig) {
 
-        if (connectorName.equals("email-otp-authenticator")) {
-            if (connectorConfig.getProperties().length == 6) {
-                boolean isMigrated = Boolean.parseBoolean(connectorConfig.getProperties()[5].getValue());
-                if  (!isMigrated && connectorConfig.getProperties()[4].getValue() != null ) {
-                    // Extract the value of the useNumericCharacters property.
-                    boolean useAlphanumericChars = !Boolean.parseBoolean(connectorConfig.getProperties()[4].getValue());
-                    // Assign the value to the alphanumeric property.
-                    connectorConfig.getProperties()[3].setValue(String.valueOf(useAlphanumericChars));
-                    connectorConfig.getProperties()[5].setValue(String.valueOf(true));
-                }
+        // If any of the following conditions are false, it simply doesn't migrate the config.
+        if (connectorName.equals(EMAIL_OTP_AUTHENTICATOR) &&
+                connectorConfig.getProperties()[3].getName().equals(EMAIL_OTP_USE_ALPHANUMERIC_CHARS) &&
+                connectorConfig.getProperties()[4].getName().equals(EMAIL_OTP_USE_NUMERIC_CHARS)) {
+
+            if (connectorConfig.getProperties()[4].getValue() != null) {
+                // Extract the value of the useNumericCharacters property.
+                boolean useAlphanumericChars = !Boolean.parseBoolean(connectorConfig.getProperties()[4].getValue());
+                // Assign the value to the alphanumeric property.
+                connectorConfig.getProperties()[3].setValue(String.valueOf(useAlphanumericChars));
             }
+        } else {
+            log.warn("Connector property migration skipped due to invalid email OTP authenticator property " +
+                    "configuration.");
         }
     }
-
 }