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I'm new on this topic and I hope to be clear... plus my english is far from being perfect, so thanks in advance.

I've configured an ADFS SSO with the WsFederation protocol. Two .net Web Applications contact the ADFS 2016 server and login successfully and now I have to develop a windows service who will be consumed by the two Web Applications like a REST API.

What's the best way to implement an authenticated communication between a Web Application and the windows service? Is there a way to federate a windows service? Should I pass the SAML token from the web application to the windows service?

many thanks!

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If you mean an API that is a REST API, that call requires a JWT not a SAML token.

In this case change WS-Fed to OpenID Connect. That returns a JWT token that can be consumed by the REST API.

OIDC samples.

If you want a service like WCF, you can do this via the WS-Fed active profile.