Recently, a customer asked me about Microsoft’s changes to throttling and service limits. In the past, they had used the multi-app registration approach and now wanted to clean it up. They also asked for clarification on how to handle backup settings and optimizations going forward.
Regarding backup throttling and the EWS → Graph API transition, I have already published two blog posts — feel free to check them out:
Microsoft EWS is dead. Long live… Graph?
Now, let’s focus on cleanup first—because multi-app registration no longer provides any performance benefits (see KB4821). Removing it is possible in both on-prem and VDC environments, but the steps differ slightly.
Step 1: Identify the App Registration IDs You Want to Remove
In VDC Backup Service you can find them here:
Veeam Data Cloud –> Microsoft 365 –> Settings –> M365 –> „Extra Backup App Registrations to Remove“
In Veeam for M365 v8 you can find them here:
Organization –> <organisation>.onmicrosoft.com –> right-click on Organization „Manage backup applications…“ –>
Step 2: Remove the Additional Applications in Entra ID
First, you must remove these extra applications in Microsoft Entra ID. You’ll find them in the Microsoft Entra admin center, and you need at least the Cloud Application Administrator.
- Log in to: https://entra.microsoft.com
- Go to App registrations
- Find the app you want to remove
- Click Deactivate
- Click Delete
Microsoft documentation:
https://learn.microsoft.com/en-us/entra/identity/enterprise-apps/deactivate-app-registration?tabs=admin-center
Step 3: Remove the App Registration Reference in Veeam
After that, you still need to remove it in Veeam.
In VDC Backup Service: “Mark as Reviewed”. Go to:
Veeam Data Cloud –> Microsoft 365 –> Settings –> M365 –> „Extra Backup App Registrations to Remove“ –> click „Mark as Reviewed“
After that, they are removed and no longer appear in the list.
In Veeam Backup for Microsoft 365 v8: “Remove”. Go to:
Organization –> <organization-name>.onmicrosoft.com –> right-click on Organization „Manage backup applications…“ –> click „Remove“
Helpful tip: PowerShell Script to Detect Multi-Application Setup
By the way, Veeam Senior Solutions Architect Chris Arceneaux wrote a PowerShell script that allows you to quickly check whether multi-application is configured in your Veeam environment.
Script on GitHub:
https://github.com/VeeamHub/powershell/tree/master/VB365-KB4821
Related community article:
https://community.veeam.com/yara-and-script-library-67/kb4821-script-to-identify-resolve-orgs-with-multiple-backup-applications-12734
After Cleanup: How to “Tune” / Optimize Performance
Now that the multi-app registrations are cleaned up, the next question is how you can further tweak performance. I already covered this in more detail in my article mentioned above, but here’s a quick list of your options.
- M365 Throttling / Limits
Make sure you understand Microsoft 365 limits. The key points:- Per minute, a maximum of 4,000 protection units can be backed up
(1 protection unit = 1 mailbox / 1 SharePoint site / 1 OneDrive) - Per hour, you are limited to 400 GB (egress + ingress)
- There are additional daily (24h) and per-minute limits depending on the tenant’s license count
- Per minute, a maximum of 4,000 protection units can be backed up
2. Limits per API Endpoint
It is quite important to know that the API limits are enforced per endpoint connection, and some services use different endpoints:
– Exchange (separate endpoint)
– OneDrive & SharePoint (shared endpoint)
– Teams (separate endpoint + SharePoint endpoint*)
You should take this into account when planning parallelism for backup jobs.
*Teams channels have their own endpoint, but many other Teams data elements often rely on the same endpoint as SharePoint, because a lot of content is stored in SharePoint and only “linked” from Teams.
More Detail:
„Dr. Backup and the Quest for the Holy Backup Performance Stream: Mastering the Latest Microsoft Throttling Changes (March 1, 2026) with Veeam Backup for Microsoft 365 v8.4 and VDC M365 (English)“
Microsoft:
https://learn.microsoft.com/en-us/sharepoint/dev/general-development/how-to-avoid-getting-throttled-or-blocked-in-sharepoint-online
3) Versioning Settings for the Backup Run
Since 04/2026 (M365 v8.4), you can influence how versioning is handled during backup. If you set it globally to “Latest Version”, API usage is significantly reduced, because only the current version is backed up—not all historical versions (which can be 20+ or even 100+ versions).
Personally, I don’t consider backing up all versions necessary in most cases, because you still capture the file as it exists at the time of the backup. That is also the long-established standard for classic VM backups and file-level backups. But as always, this is something each organization should evaluate for itself.
4) Different Licensing Models for Scaling (VDC)
If you use Veeam Data Cloud (VDC), you can license the product in three editions: Foundation, Advanced, Premium.
The Foundation edition uses the traditional Export API and can reach speeds of about 1–2 TB per day.
Backing up 50 TB can therefore take roughly 2–3 weeks.
The Premium edition uses the Microsoft 365 Backup Storage APIs, enabling unthrottled backup and restore processes.
Speeds of 3–5 TB per hour can be achieved, so 50 TB can be protected within a single day.
Important: You can also mix licenses, allowing you to provide different backup/restore speeds for specific users or particular locations/departments.
Sources for the different editions:
https://www.veeam.com/de/products/saas/backup-microsoft-office-365.html#comparison
https://www.veeam.com/veeam_data_cloud_m365_comparison_ds.pdf
https://helpcenter.veeam.com/docs/vdc/userguide/m365_licensing.html
