API with JWT trying to authenticate without OWIN

Hi so I am new to all of this so please bare with me if this is a silly question. I have so far figured out how to generate a JWT and validate it (created a little program while learning). I have also learnt how to create a web api (again created a little program which queries the db and shows in postman). What I am trying to accomplish is that we want to create api so our customers can create their own site/apps. we are using JWT so how would I tell all my controllers to first go off and validate the JWT coming in the url. It will also be base64 encoded with the claims being encrypted. However I know what i need to do with all of that as I have been playing around. My issue is how do i tell a call to one of what will be many controllers to first go off and validated the token. I have looked online and it seems that a lot use OWIn which i do not have the luxury off.

Thanks