a.ProtocolMessage.IssuerAddress = "https://login.windows.net/common/wsfed";

multiorg.owin.cs

app.UseCookieAuthentication(new CookieAuthenticationOptions
            {
                AuthenticationType = WsFederationAuthenticationDefaults.AuthenticationType,
             
            });
            app.UseWsFederationAuthentication(new WsFederationAuthenticationOptions
            {
               
                TokenValidationParameters = new System.IdentityModel.Tokens.TokenValidationParameters
                {
                   
                    // I will update this demo as more information is avalibe.
                    //ValidateIssuer  = false -> this causes IssuereValidator to not be run. 
                    //UPDATE Bug has been confirmed that this is not working as intented.
                    //UPDATE2 This works when a 3th party organizational user signs in, if returning false the user will not be signed in
                    //but it gives a YSOD right now instead of a user friendly error.
                    IssuerValidator = (issuer, token) =>
                    {
                        return true;
                        return false; // it still sign in the user even though its false.

                        //     return DatabaseIssuerNameRegistry.ContainsTenant(issuer);

                    }
                },
                IssuerAddress = "https://login.windows.net/common/",
                Wtrealm = "https://demo009.s-innovations.net",
                Wreply = "https://localhost:44309/",
                MetadataAddress = "https://login.windows.net/802626c6-0f5c-4293-a8f5-198ecd481fe3/FederationMetadata/2007-06/FederationMetadata.xml",
                Notifications = new WsFederationAuthenticationNotifications
                {
                    AuthenticationFailed = async (a) =>
                    { },
                    MessageReceived = async (a) =>
                    { },
                    RedirectToIdentityProvider = async (a) =>
                    {
                       // a.ProtocolMessage.SetParameter("site_id", "501358"); //this is the oauth site id for mail discovery
                        a.ProtocolMessage.IssuerAddress = "https://login.windows.net/common/wsfed";
                        a.ProtocolMessage.Parameters.Add("id", "500879");
                    },
                    SecurityTokenReceived = async (a) =>
                    { }
                    ,
                    SecurityTokenValidated = async (a) =>
                    { }

                },
                
            });