OWIN authenticate MVC an web API together and individually

I'm building a web application which use ASP.NET MVC and Web Api. I started building it using the VS 2013 SPA template which use OWIN. In this way the MVC application use the auth cookies and the web api the bearer token to authenticate. But both of them (cookie and token) are set up during the form logon page.

Now I want that other clients can authenticate individually only using the web api to getting the token.

I tried more times making calls to the /token end point or the /account/authorize (which is set up in the SPA template), but with no happy results.

Do I have to configure OWIN in an other way, or what am I doing wrong?