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In the Azure portal on the properties of a user I can see the employeeID populated. When I run Get-MGUser is does not list the information and most attributes which are populated in the GUI are blank. I have tried to specify the employeeid property, uninstalled reinstall graph etc.. same result. I have read other having the same issue but all the their suggestions have not worked for me.
A cloud-based identity and access management service for securing user authentication and resource access
You didnt mention how you are querying :)
This shows it for me:
Get-MgUser -UserId <UserPrincipalName> -Property EmployeeID | select EmployeeID