When you’re attempting to administer Skype for Business Online or Lync Online, you’re likely going to use the Lync Online Module for Windows Powershell, or the Skype for Business Online Windows Powershell Module.

When I ran this for a customer that has two federated domains, I received an error:

$env:PSModulePath += ";C:\Program Files\Common Files\Skype for Business Online\Modules"
ipmo SkypeOnlineConnector
$session = New-CsOnlineSession -credential $cred
Get-CsPowerShellEndpoint : The remote server returned an error: (406) Not Acceptable.
At C:\Program Files\Common Files\Skype for Business Online\Modules\SkypeOnlineConnector\SkypeOnlineConnectorStartup.psm1:94 char:26
+ ... $targetUri = Get-CsPowerShellEndpoint -TargetDomain $adminDomain
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ CategoryInfo : NotSpecified: (:) [Get-CsPowerShellEndpoint], WebException
+ FullyQualifiedErrorId : System.Net.WebException,Microsoft.Rtc.Management.OnlineConnector.GetPowerShellEndpointCmdlet

Messing around a bit, I discovered that it did work for another administrator, it ended up being the UPN suffix. When I changed the login domain (UPN) of the user that couldn’t log in to the DEFAULT domain in Office 365 instead of one of the extra domains and waited a while until it was propagated to Skype for Business Online, I could log in without issues.