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I've created a custom STS and have setup trust with SharePoint via New-SPTrustedIdentityTokenIssuer. I can use Central Admin to configure a Web Application to use both NTLM and the STS, however I can't do that via PowerShell.

Is there a PowerShell command to do that? Set-SPWebApplication has the AuthenticationMethod and AuthenticationProvider parameters, but if I specify both, only AuthenticationProvider is applied, i.e. Windows Authentication is unticked.

Any help greatly appreciated!

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In case this helps anyone else (or me in the future) you can do this with:

$winAp = new-SPAuthenticationProvider -UseWindowsIntegratedAuthentication
$stsAp = Get-SPTrustedIdentityTokenIssuer "YourSTS"
Set-SPWebApplication -Identity $webApp -AuthenticationProvider $stsAp, $winAp -Zone "Default"

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