You can surely do this with open source. So I think it is possible with IIS as well. Assuming you mean ** TLS Client Authentication** (2-way SSL).
With Apache2 Client Authentication works by exposing the authenticated user's data to your web application. Here is a sample app I put together to demo TLS Client Authentication. Here are the relevant pieces.
Config to use TLS Client Auth (this works w/ a single root, but you can also use multiple CAs by specifying
SSLCACertificatePath instead of
SSLOptions +StdEnvVars exposes the client certificate's data as an environment variable to your PHP script. You can then access it like so.
This way you can verify which client is authenticating in your web application. I am not familiar with how IIS handles these cases, but I think it is supported in some way. The key is to have it configured in a way to use multiple CAs when authenticating the clients. This post should help.
Alternatively, you can check out other authentication methods that provide a similar level of protection that TLS Client Certificates do.