Hi Martijn,
Thanks for your update.
Currently, I suggest you type the Team Site full address in browser to see if you can access the Team Site. The address is http: yourdomain.sharepoint.com/teamsite by default.
Moreover, please login Microsoft Online Portal (MOP), click Users under Management in the Admin page, select the user and then click Edit, check the SharePoint Online license of the Administrator in the Licenses section. If it was not selected, select it. If it was selected, unassigned that, wait for 15 minutes, and then reassigned that to have a try.
Image may be NSFW.
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In additional, could you please provide more detailed information about what you have delete in the team site?
Thanks,
Eric Sun