Troubleshoot Azure AD Certificate-Based Authentication issues

The Certificate-Based Authentication feature in Microsoft Azure Active Directory (AD) for iOS or Android devices allows Single Sign-On (SSO) by using X.509 certificates. By enabling this feature, you can log in to accounts or services without having to enter a user name and password when you connect to your Exchange Online account or Office mobile applications.

This article provides information to help you troubleshoot Certificate-Based Authentication issues.

Original product version:   Azure Active Directory
Original KB number:   4032987

General requirements

  • Certificate-Based Authentication supports only Federated environments by using Modern Authentication (ADAL). The one exception is Exchange ActiveSync (EAS) for Exchange Online that can be used by Managed Accounts.
  • The user certificate that's issued in the user's profile requires the user's routable email address to be listed in the Subject Alternative Name. This can be in either the UserPrincipalName or RFC822 format. Azure AD maps the RFC822 value to the Proxy Address attribute in the directory.

Determine if Certificate-Based Authentication works on Azure portal

  1. Browse to the Azure portal from the device for testing the Certificate-Based Authentication.


    The browser cache must be cleared before you try the connection in order for the user to see the certificate approval prompt.

  2. Type the user's email address. This redirects to the ADFS authentication page.

  3. Instead of typing a password (if the forms-based authentication method is enabled in ADFS), select Sign in using an X.509 certificate, and approve the use of the client certificate when you are prompted.

    If no certificate approval prompt is received after you clear the browser cache on a device, follow these steps:

    1. Verify that the user certificate and the issuing certificate authority root certificates are installed on the device.
    2. Verify that TCP port 49443 is open on the ADFS/Web Application Proxy servers, and that the certificate chain of the issuing certificate authority is installed on all ADFS/Web Application Proxy servers.

Determine if Azure AD is correctly configured

  1. Run the following PowerShell command to Install the Azure Active Directory PowerShell (Preview) module:

    Install-Module AzureAD
  2. To create a trusted certificate authority, use the New-AzureADTrustedCertificateAuthority cmdlet, and set the crlDistributionPoint attribute to a correct value.


    When you create the TrustedRootCertificateAuthority objects in Azure AD, the CRL URLs that are defined within the .CER file are not used. The CrlDistributionPoin and DeltaCrlDistributionPoint values must be manually populated by a web location where Azure AD can access the CRLs. The CRL paths within the issued certificates do not have to contain the URLs that are accessible to Azure AD. Also, large CRLs that take more than 15 seconds to download should be put on a faster link, such as Azure Storage, to avoid caching delays that can cause intermediate authentication failures.

    $cert=Get-Content -Encoding byte "[LOCATION OF THE CER FILE]"
    $new_ca=New-Object -TypeName Microsoft.Open.AzureAD.Model.CertificateAuthorityInformation $new_ca.AuthorityType=0 $new_ca.TrustedCertificate=$cert
    $new_ca.crlDistributionPoint="<CRL Distribution URL>"
    New-AzureADTrustedCertificateAuthority -CertificateAuthorityInformation $new_ca
  3. Make sure that the following values are correctly defined on the TrustedCertificateAuthority objects according to the following guidelines:

    • All CrlDistributionPoin and DeltaCrlDistributionPoint URLs must be accessible from the Internet by the client devices and the ADFS and Web Application Proxy servers.

    • The *.CER for the Root CA should be listed as AuthorityType = RootAuthority.

    • The *.CER for the Intermediate CA should be listed as follows:

      AuthorityType = IntermediateAuthority
      AuthorityType = 0 = RootAuthority
      AuthorityType = 1 = IntermediateAuthority


    To make changes to these objects, see Configure the certificate authorities.

  4. Run the following commands to make sure that the ADFS settings are not set to PromptLoginBehavior: true. Otherwise, users will be prompted to enter their user name and password for some modern apps.

     Get-MSOLDomainFederationSettings -DomainName


    This occurs because some modern apps send prompt=login to Azure AD in their request. Azure AD translates this in the ADFS request to wauth=usernamepassworduri (this tells ADFS to do username/password authentication) and wfresh=0 (tells ADFS to ignore the SSO state and do a fresh authentication). If users have to use Certificate Based Authentication, the PromptLoginBehavior must be set to False.

    To disable PromptLoginBehavior on the Azure AD domain, run the following command:

    Set-MSOLDomainFederationSettings -domainname <domain> -PromptLoginBehavior Disabled

Determine if the ADFS and Web Application Proxy configurations are configured correctly

  1. Certificate-Based Authentication requires ADFS 2012R2 or a later version, and it must use Web Application Proxy.


    Using a third-party Web Application Proxy is not supported unless it supports all the MUSTs in the MS-ADFSPIP protocol document.

  2. The Root *.CER file must be in the computer's Trusted Root Certificate Authority\Certificates container. Also, all Intermediate *.CER files must be in the computer's Intermediate Root Certificate Authority\Certificates container. You can verify this by running certlm.msc or by running the following certutil.exe commands at an elevated command prompt:

    certutil -verifystore root
    certutil -verifystore CA**
  3. The client devices, the ADFS servers, and the Web Application Proxy must be able to resolve the CRL endpoints that exist on the Intermediate CA *.CER and on the user certificates that were issued to the user profile on the devices.

    To verify that the ADFS servers and the Web Application Proxy can resolve these, follow these steps:

    1. Export the Intermediate CA *.CER:
      1. View the computer certificate store. To do this, run certlm.msc, expand \Intermediate Certification Authorities\Certificates, and then double-click the Intermediate CA certificate.
      2. Click the Details tab, and then click the Copy to file button.
      3. Click Next two times and accept all the defaults in the wizard.
      4. Specify a file name and location, click Next, and then click Finish.
    2. On the issuing CA, export one of the user certificates that was issued to a device. To do this, follow these steps:  
      1. Run certsrv.msc, and then select the Issued Certificates node.

      2. In the Issued Common Name column, locate the certificate that was issued to the user who cannot connect.

      3. Double-click the certificate, and then click the Details  tab to export the certificate to a *.CER file.


        If more than one certificate is issued to the user, locate the serial number for the certificate on the Details  tab, and verify that it matches the certificate on the device.

      4. Download PSEXEC.EXE, and then copy psexec.exe together with the *.CER files from the Intermediate CA and user to all ADFS and Web Application Proxy servers.

      5. Open a new command prompt in the SYSTEM security context. To do this, open an elevated command prompt for each server, and then run the following command:

        psexec -s -i -d cmd.exe
      6. At the new command prompt, run the following commands to determine whether the CRL can be accessed:

        certutil.exe -verify -urlfetch SubCA.cer > %computername%_%username%_SubCA.txt
        certutil.exe -verify -urlfetch usercert.cer > %computername%_%username%_usercert.txt
      7. In the output, check the ---------------- Certificate CDP ---------------- section, and determine whether all endpoints can be resolved.

      8. If the ADFS servers cannot resolve the HTTP URL, make sure that the Group Managed Service Accounts that ADFS is running under has access through the firewall and proxy. The Web Application Proxy service runs under Network Service, so the ComputerName$ account requires access through the firewall and proxy.

  4. Pass Through Claims for serialNumber and issuer must be configured for the Active Directory Claims Provider Trust and for the Microsoft Office 365 Identity Platform Relying Party Trust. These can be retrieved from the ADFS servers by running the following PowerShell commands at an elevated prompt:

    Get-AdfsClaimsProviderTrust -Name "Active Directory"
    @RuleTemplate = "PassThroughClaims"
    @RuleName = "<serialnumber AD for cert based auth>"
    c:[Type ==]
      => issue(claim = c);
    @RuleTemplate = "PassThroughClaims"
    @RuleName = "<Issuer AD for cert based auth>"
    c:[Type ==]
      => issue(claim = c);
    Get-AdfsRelyingPartyTrust -Name "Microsoft Office 365 Identity Platform"
    @RuleTemplate = "PassThroughClaims"
    @RuleName = "<serialnumber RP for cert based auth>"
    c:[Type ==]
      => issue(claim = c);
    @RuleTemplate = "PassThroughClaims"
    @RuleName = "<Issuer RP for cert based auth>"
    c:[Type ==]
      => issue(claim = c);
  5. Because most devices that use certificate authentication are likely to be located on the extranet (out of the corporate network), you could enable Certificate-Based Authentication only for the extranet or also for the Intranet, as necessary. To determine whether the "Certificate Authentication" method is enabled for either or both options, run the following cmdlet from an elevated PowerShell command prompt:

    ----------Output sample----------
    AdminName                          : Certificate Authentication
    AllowedForPrimaryExtranet          : True
    AllowedForPrimaryIntranet          : True
    AllowedForAdditionalAuthentication : True
    AuthenticationMethods              : {urn:ietf:rfc:2246, urn:oasis:names:tc:SAML:1.0:am:X509-PKI,
    Descriptions                       : {}
    DisplayNames                       : {}
    Name                               : CertificateAuthentication
    IdentityClaims                     : {}
    IsCustom                           : False
    RequiresIdentity                   : False
    1. Locate the AdminName entry that is named Certificate Authentication.
    2. Verify that AllowedForPrimaryExtranet is set to True.
    3. Optionally, you can also set AllowedForPrimaryIntranet to True if you want Certificate-Based Authentication from Intranet users.
    4. Click the Details tab, and then click the Copy to file button.
  6. TCP port 49443 must be accessible between the client device and ADFS,  also between the client device and Web Application Proxy servers. To verify that TCP 49443 is listening and bound to ADFS on the ADFS servers and Web Application Proxy, run the following command:

    netsh http show urlacl > %computername%_49443.txt

    If the TCP port 49443  is accessible, you should see output such as the following:

    Reserved URL: https://<URL>:49443/adfs/
    User: NT SERVICE\adfssrv
    Listen: Yes
    Delegate: Yes
    SDDL: D:(A;;GA;;;S-1-5-80-2246541699-21809830-3603976364-117610243-975697593)
  7. On a client device, try to connect to the CertificateTransport endpoint. For example, use the following URL for


    If the endpoint is accessible and listening, the connection attempt should spin indefinitely while it waits for an answer.

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