When adding a Microsoft 365 organization with Modern Authentication to Veeam Backup for Microsoft 365, there is an option to enable "Allow for using legacy authentication protocols." When this checkbox is not selected, Veeam Backup for Microsoft 365 will use a mode referred to as Modern App-Only Authentication.

When using Modern App-Only Authentication, the following limitations apply:

Backup

• Discovery Search mailboxes are not supported.
  
  ^New Support for Discovery Search mailboxes was added in Veeam Backup for Microsoft 365 7 P20230704 (7.0.0.3968).
• Public Folder mailboxes are not supported.
  As an alternative to Public Folders, Microsoft recommends using Microsoft 365 Groups. Information about migrating can be found in Migrate your public folders to Microsoft 365 Groups in Exchange Online.
  
  ^New Support for Public Folder mailboxes was added in Veeam Backup for Microsoft 365 7 P20230704 (7.0.0.3968).
• Dynamic Distribution groups are not supported.
  
• The type property for shared and resource/equipment mailboxes cannot be resolved. Such mailboxes will be available for backup with a general ‘User’ type (Note: This limitation only applies to creating a backup jobs and does not affect licensing).
• SharePoint Web Parts can only be backed up if their ‘exportmode’ property is enabled. Non-exportable Web Parts are not supported. To prevent issues processing WebParts, review and implement the solution documented in KB4091.

Restore

• OneNote restore is not supported.
• SharePoint Web Part customized template cannot be preserved upon a restore. All Web Parts will be restored with the default template.
• The ‘Allow multiple responses’ setting in survey lists within team modern sites is not preserved upon a restore.
  

PowerShell

• The ‘Measure-VBOOrganizationFullBackupSize’ cmdlet is not supported.

For a complete list of considerations and known limitations of Veeam Backup for Microsoft 365, review: Considerations and Limitations