Can't get UserManager from OwinContext in apicontroller

I really misunderstood your question earlier. You are just missing some using statements, I think.

The GetOwinContext().GetUserManager<ApplicationUserManager>() is in Microsoft.AspNet.Identity.Owin.

So try add this part:

using Microsoft.AspNet.Identity.Owin;
using Microsoft.AspNet.Identity; // Maybe this one too

var manager = HttpContext.Current.GetOwinContext().GetUserManager<UserManager<User>>();

This extension method may be a better solution if you want to unit test your controllers.

using System;
using System.Net.Http;
using System.Web;
using Microsoft.Owin;

public static IOwinContext GetOwinContext(this HttpRequestMessage request)
{
    var context = request.Properties["MS_HttpContext"] as HttpContextWrapper;
    if (context != null)
    {
        return HttpContextBaseExtensions.GetOwinContext(context.Request);
    }
    return null;
}

Usage:

public ApplicationUserManager UserManager
{
   get
   {
      return _userManager ?? Request.GetOwinContext().GetUserManager<ApplicationUserManager>();
   }
   private set
   {
      _userManager = value;
   }
}

This single line of code saved my day...

       var manager = 
       new ApplicationUserManager(new UserStore<ApplicationUser>(new ApplicationDbContext()));

You can use it within a controller action to get an instance of UserManager.