While we are updating the XML through the admin portal, we are getting the duplicate entry in the entra.microsoft.com (App registration)

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While we are updating the XML through the admin portal, we are getting the duplicate entry in the entra.microsoft.com (App registration)

Bhargavi Venkata Reddy 0

We are getting a duplicate entry in the entra portal while we are updating the existing xml by Admin.

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Answer 1

Bhargavi Venkata Reddy 0

But we didn't change the entraid we have changed the only version number and removed the scope inside the webaddininfo and reuploaded the XML at that time we are getting the Duplicate XML in the entra app registration.

Hani-Ng 11,315 Reputation points Microsoft External Staff Moderator

2026-05-07T23:44:35.1933333+00:00
Hi Bhargavi Venkata Reddy

Thank you so much for that clarification! Mentioning <WebApplicationInfo> and the version number is very helpful. Since you mentioned that specific tag, it sounds like you are uploading an Office/M365 Add-in XML manifest (likely through the Microsoft 365 Admin Center), rather than a standard SAML metadata file.

When you deploy or update an Add-in, the Microsoft 365 deployment engine reads that <WebApplicationInfo> section to automatically set up SSO and permissions in Entra ID.

When you remove or change a scope in the XML, the automation notices the permissions have changed. Instead of modifying the existing Entra app, it plays it safe and spins up a brand-new App Registration. It does this by design because changes to scopes usually require fresh Admin Consent, so the system creates a duplicate to avoid breaking any existing consent policies for your users.

If you want to try and force it to use the existing app, you can try syncing them up manually first:

Update Entra ID manually first: Go directly to entra.microsoft.com > App Registrations > open your existing app. Navigate to API permissions and Expose an API and manually add/remove the scopes there to match your new XML.

Re-upload the XML: Once the existing Entra ID app perfectly matches your new XML scopes, go to the Microsoft 365 Admin Center and update the Add-in XML.

Note: If the Microsoft 365 Admin Center still generates a duplicate after doing this, it is a hardcoded behavior of the Integrated Apps deployment tool when it detects scope changes. In that case, the best practice is to grant Admin Consent to the new App Registration, verify the Add-in works, and then delete the old/unused App Registration.

I hope this helps.
Hani-Ng 11,315 Reputation points Microsoft External Staff Moderator

2026-05-11T07:06:12.9733333+00:00

Hi Bhargavi Venkata Reddy

Just checking in to see if you've had a chance to check my previous reply. Please let me know if you have any further questions.

Answer 2

Hi Bhargavi Venkata Reddy

Based on my research and understanding, this behavior occurs when Entra ID interprets the updated XML file as a completely new application rather than an update to your current one. When a new SAML/Enterprise Application is created, Entra ID automatically generates a corresponding App Registration, which is why you see duplicates there.

This usually happens for:

Identifier Mismatch: The Entity ID (Identifier) in your new XML differs slightly from the existing app (even a minor change like an extra slash / or different capitalization will trigger a duplicate).
Upload Method: The XML is being uploaded via a "Create new application" flow rather than being applied directly to the existing app. (Note: If a third-party admin portal is pushing this XML automatically via API, it may be sending a "Create" command instead of an "Update" command).

To safely update your metadata moving forward, you can follow these steps:

Go to Microsoft Entra ID > Enterprise Applications.
Search for and click on your existing application.
Select Single sign-on > SAML from the left menu.
Click Upload metadata file directly at the top of this page. (Ensure the Entity ID in the XML exactly matches what is currently in Entra).

Before deleting anything, please check the Sign-in logs and Users and groups assignments for both the old and new applications. Once you verify which application is actively handling your authentication traffic, you can safely delete the unused duplicate.

For your information:

Enable SAML single sign-on for an enterprise application - Microsoft Entra ID | Microsoft Learn

Apps & service principals in Microsoft Entra ID - Microsoft identity platform | Microsoft Learn

I hope this information helps, and if you have any question, please feel free to ask via comment section.

Note: Please follow the steps in our documentation to enable e-mail notifications if you want to receive the related email notification for this thread.

I hope this information helps.

Bhargavi Venkata Reddy 0 Reputation points

2026-05-07T08:09:07.7666667+00:00

But the issue is getting even without changing the entra Id we just changed the scope and updated the existing XML still we are seeing the duplicate one.

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While we are updating the XML through the admin portal, we are getting the duplicate entry in the entra.microsoft.com (App registration)

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