Is there Application_End from Global.asax in Owin?

AppProperties, found in Microsoft.Owin.BuilderProperties, exposes the CancellationToken for OnAppDisposing.

You can get this token and register a callback to it

public class Startup
{
    public void Configuration(IAppBuilder app)
    {
        var properties = new AppProperties(app.Properties);
        CancellationToken token = properties.OnAppDisposing;
        if (token != CancellationToken.None)
        {
            token.Register(() =>
            {
                // do stuff
            });
        }
    }
}