Removing onmicrosoft.com Domain from SharePoint online

It somewhat depends. The primary question is are there in fact two accounts in Azure AD?

Let’s parse out possible explanations based on the potential answers to that question:

Yes there are two accounts in Azure AD and that’s intentionally done

If there are two accounts then out of the box people picker will pick up both accounts. Based on some initial research, I wasn’t able to find a way to filter out users from a specified domain, but that could warrant further investigation.

Yes there are two accounts in Azure AD and that’s not intentionally done

If the user has two accounts, but you don’t want them to have two accounts, remove the redundant account and clear browser cache.

No there’s only one account for this user in Azure AD

Clear browser cache, duplicate account is most likely being stored there.