I came across a problem for seeding the database with Identity v2. I separated out the IdentityModel from the MVC5 project to my Data Access Layer where I setup EF Migration
This is the way to avoid using an OWIN context:
protected override void Seed(Repository.DataContext.IdentityDb context)
var roleStore = new RoleStore(context);
var roleManager = new RoleManager(roleStore);
var userStore = new UserStore(context);
var userManager = new UserManager(userStore);
var user = new ApplicationUser { UserName = "sallen" };
userManager.Create(user, "password");
roleManager.Create(new IdentityRole { Name = "admin" });
userManager.AddToRole(user.Id, "admin");
}