Change Certificate on Windows Server 2012 R2 Web Application Proxy

With ADFS 3.0 and Web Application Proxy the installation of IIS is not required and necessary. The binding for certificates on the ADFS and WAP service can be done with PowerShell. In this example the same certificate will be used for ADFS and all WAP applications.

The desired certificate must have been installed into the local machines certificate store and the hash value of the certificate will be used to reference the certificate. To list all available certificates run:

dir Cert:\LocalMachine\My

example:

Thumbprint                                Subject
----------                                -------

9450B39AAAE6F203DD68AC1EA1D8D46A8C581E41  CN=certold.mydomain.com
921461C2FF106D4A50A6F3574D1CC25A7D4451B9  CN=certnew.mydomain.com

Now run the PowerShell commands to bind the new certificate:

get-WebApplicationProxyApplication DRS | set-WebApplicationProxyApplication -ExternalCertificateThumbprint 921461C2FF106D4A50A6F3574D1CC25A7D4451B9

get-WebApplicationProxyApplication Workfolders | set-WebApplicationProxyApplication -ExternalCertificateThumbprint 921461C2FF106D4A50A6F3574D1CC25A7D4451B9

Set-WebApplicationProxySslCertificate -Thumbprint 921461C2FF106D4A50A6F3574D1CC25A7D4451B9

Now restart the ADFS service

stop-service "Active Directory Federation Services"

start-service "Active Directory Federation Services"

For verification  you can run these commands and verify that the new hash is active:

get-WebApplicationProxyApplication DRS

get-WebApplicationProxyApplication Workfolders

get-WebApplicationProxySslCertificate

or 

netsh http show ssl

How to archive and un-archive certificates

You are might aware that certificates can be flagged archived on a Windows machine. That has nothing (as in nada) to do with key archiving what is performed if configured on the Certification Authority.
The archive flagged is used to make certificates invisible to applications without deleting them from a user or machine store. E.g. auto-enrollment sets this flag to an certificate if a new certificate has been enrolled.
In this post I want show you how to set and unset this flag.

First of all we want see if we have a certificate in the certificate store with the archive flag set. I work on my machine as local administrator and so should you.

1. Open for that a MMC and add the Certificate snap-in for either your user or the local machine, or both if you like.

Then enable show archived certificates. That is like an advanced view setting that you might know from Active Directory Users and Computers.

Note: You have to enable the Archived certificate view for each snap-in separately. So in the picture above I made that for Certificates - Current user and for Certificates (Local Computer)


Now you see archived certificates in the MMC

Note the letter A at the end. That is the sign that this certificate is flagged archived.


2. You can do the same by running a certutil command. The MMC does not give you an option to set the flag from there. So you have to use certutil to do that, see below.


Use certutil to see all certificates

certutil.exe -store my

will show you all certificates in the local machine store

...
================ Certificate 4 ================
Archived!
Serial Number: 3dc344f3e2cf6dab48d7085ecd1bb849
Issuer: CN=localhost
 NotBefore: 6/13/2012 2:17 PM
 NotAfter: 6/12/2022 5:00 PM
Subject: CN=localhost
Signature matches Public Key
Root Certificate: Subject matches Issuer
Template:
Cert Hash(sha1): 80 3e 7f 62 5a be 5b 14 52 e3 65 dd 72 4d 59 98 cb 8a 30 d3
  Key Container = IIS Express Development Certificate Container
  Unique container name: fad662b360941f26a1193357aab3c12d_42f2ea6e-c662-4d0b-8b56-2f094a3a3dc9
  Provider = Microsoft RSA SChannel Cryptographic Provider
Encryption test passed
....


So that certificate is number 4 in the certificate store. Lets write this down for later.


3. We will use certutil for un-archiving the certificate (and we can use it for archiving as well).

Here the file to set the archive flag.
- Create a new file with notepad and call it archive_set.inf
- paste these two lines to the archive_set.inf file

[Properties]
19 = Empty ;

- save the file

Here the file to remove the archive flag
- Create a new file with notepad and call it archive_remove.inf
- paste these 2 lines to the archive_remove.inf file

[Properties]
19 =          ;

- save the file

4. Now you can toggle the archive flag as you desire:

Now you need the number you have taken down from step 2 or use the certificate serial number instead.


flag on

certutil.exe -repairstore my 4 archive_set.inf


flag off

certutil.exe -repairstore my 4 archive_remove.inf





See also http://blogs.technet.com/b/pki/archive/2007/02/22/how-to-manually-set-the-archive-flag-for-certifictes.aspx