Start-Transcript c:\temp\msolfederation_check_log.txt
# Getting the local AD FS server address:
$stsaddress = ""
$stsaddress = (Get-AdfsEndpoint -AddressPath /adfs/ls/).FullUrl
$stsaddress = $stsaddress -replace "https://","" -replace "/adfs/ls/",""
write-host "The local AD FS address is $stsaddress"
$federateddomains = Get-MsolDomain | where{$_.authentication -eq "Federated"}
foreach($feddomain in $federateddomains)
{
# Clearing the variables
$certmatch = ""
$feddomainname=""
$fedinfo=""
$fedinfosts=""
# Setting the domainname of this domain
$feddomainname=$feddomain.name
if($feddomain.rootdomain)
	{
		write-host -ForegroundColor Yellow "$feddomainname is a subdomain, skipping check"
		$feddomainname >> "C:\temp\FedDomains - Subdomains.txt"
	}
else
	{
	write-host -NoNewline "Checking Federation for domain $feddomainname..."
	# Getting federation information for this domain
	$fedinfo = Get-MsolFederationProperty -domainname $feddomainname -ErrorAction SilentlyContinue
	if($fedinfo)
		{
			# Getting the STS info for this domain that can be in either two of the resulting array
			if($fedinfo.source[0] -eq "Microsoft Office 365") { $fedinfosts = $fedinfo.tokensigningcertificate[0].subject }
			if($fedinfo.source[1] -eq "Microsoft Office 365") { $fedinfosts = $fedinfo.tokensigningcertificate[1].subject }
			# Now we check if the thumbprints match
			if($fedinfo.tokensigningcertificate[0].Thumbprint -eq $fedinfo.tokensigningcertificate[1].Thumbprint) { $certmatch = "1" } else { $certmatch = "" }
			if($fedinfosts -like "*$stsaddress*")
				{
					write-host -NoNewLine " Federated to "
					write-host -NonewLine -foregroundcolor Green "this AD FS service"
					if($certmatch -eq "")
						{
							write-host -ForegroundColor Red " but certificates do not match!!!"
							# You could try to execute the below command to update the Federation information # if you feel safe in this.
							# Update-MsolFederatedDomain -DomainName $feddomainname -SupportMultipleDomain
							$feddomainname >> "C:\temp\FedDomains - ADFS Match - Cert Mismatch.txt"
						}
					else
						{
							write-host -ForegroundColor Green " and certificates do match."
							$feddomainname >> "C:\temp\FedDomains - ADFS Match - Cert Match.txt"
						}
					$feddomainname >> "C:\temp\FedDomains - domains federated to this ADFS.txt"
				}
			else
				{
					write-host -NoNewLine " Federated to "
					write-host -foregroundcolor Yellow "another AD FS instance"
					$feddomainname >> "C:\temp\FedDomains - ADFS Mismatch.txt"
				}
		}
	}
}
Stop-Transcript