Hi @Gal, Ofer , thank you for posting in the Q&A forum.
Quoting the document you mentioned:
When you first launch the SharePoint Migration Tool (SPMT), you are prompted for your Microsoft 365 username and password. The credentials you provide will be to the migration destination.
The supported authentication method listed under, including "Client certificate authentication", are meant for the on-premises server. Azure registered app authentication cannot be used in this scenario.
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