How to use Windows authentication on ASP.NET Core subpath only?

In order to have a certain page/action method secured via Windows authentation, specify the corresponding authentication scheme in the action methods Authorize attribute.

[Authorize(AuthenticationSchemes = IISServerDefaults.AuthenticationScheme)]
public IActionResult UsingWindowsAuthentication()

Make sure to have Windows authentication enabled on your website.
In order to use other authentication schemes, e.g. "Individual Accounts", anonymous authentication is also enabled.

The controllers and/or action methods that must not use Windows Authentication have the default scheme specified.
For example, for an ASP.NET Core MVC project that uses the out of the box "Individual Accounts" authentication type as default authentication method, that is Identity.Application.

[Authorize(AuthenticationSchemes = "Identity.Application")]
public IActionResult Index()

See the documentation about how to set up and configure multiple authentication schemes.

Another way using endpoint routing:

We have an application schema for the application that will be used all over the app called eavfw.

Using a custom endpoint here called login/ntlm with metadata new AuthorizeAttribute(NegotiateDefaults.AuthenticationScheme) its only allowed to be visited by a valid windows authenticated user.

Here we then create the user in our DB using its AD username.

    endpoints.MapGet("/.auth/login/ntlm", async httpcontext =>
    {
        var loggger = httpcontext.RequestServices.GetRequiredService<ILogger<Startup>>();
        var windowsAuth = await httpcontext.AuthenticateAsync(NegotiateDefaults.AuthenticationScheme);
        
        if (!windowsAuth.Succeeded)
        {
            loggger.LogWarning("Not authenticated: Challening"); 
        }
        if (windowsAuth.Succeeded)
        {
            loggger.LogWarning("Authenticated");
           
            var name = string.Join("\\", windowsAuth.Principal.Claims.FirstOrDefault(c => c.Type.EndsWith("name")).Value.Split("\\").Skip(1));

            var context = httpcontext.RequestServices.GetRequiredService<DynamicContext>();
            var users = context.Set<SystemUser>();
            var user = await context.Set<SystemUser>().Where(c => c.PrincipalName == name).FirstOrDefaultAsync();
            if (user == null)
            {
                user = new SystemUser
                {
                    PrincipalName = name,
                    Name = name,
                    // Email = email,
                };
                await users.AddAsync(user);
                await context.SaveChangesAsync();
            }
             
            var principal = new ClaimsPrincipal(new ClaimsIdentity(new Claim[] {                                  
                       new Claim(Claims.Subject,user.Id.ToString())
                    }, "ntlm"))
            {

            };

            await httpcontext.SignInAsync("ntlm",
                 principal, new AuthenticationProperties(
                            new Dictionary<string, string>
                            {
                                ["schema"] = "ntlm"
                            }));

            httpcontext.Response.Redirect("/account/login/callback");
        }
      

    }).WithMetadata(new AuthorizeAttribute(NegotiateDefaults.AuthenticationScheme));

using a auxility authentication cookie, we can now make it such that specific areas of our app that requires windows authentication, it can simply rely on Authorize("ntlm") as it automatically forward the authenticate call to check if already signin, and it as part of the signin call in the endpoint above actually sign in eavfw.external before it redirects to the general account callback page that will do some final validation before signing in eavfw from the eavfw.external cookie

            services.AddAuthentication().AddCookie("ntlm", o => {
                o.LoginPath = "/.auth/login/ntlm";
                o.ForwardSignIn = "eavfw.external";
                o.ForwardAuthenticate = "eavfw";
            });

So there are a few ways to extend and use the authentication system in auth core depending on how MVC framework heavy your application is.

Just thought I'd share this tidbit of information:

First off, just because you installed Windows Authentication with Server Manager, doesn't mean it's enabled in IIS. It's NOT enabled, by default.
You have to open IIS Manager, click on your server (NOT the website - the name of the server machine hosting IIS). Then click on Authentication - you will see "Windows Authentication" is disabled. Enable it. Now it will work.

Check this is correctly set first, before making other config changes. The default project for dotNet5 and dotNet6 will work w/o any modifications if IIS is correctly configured for Windows Authentication.