Code to go with my comment at: http://bitoftech.net/2014/10/27/json-web-token-asp-net-web-api-2-jwt-owin-authorization-server/

gistfile1.cs

public void ConfigureOAuth(IAppBuilder app)
{
    var issuer = "<the_same_issuer_as_AuthenticationServer.Api>";

    // Api controllers with an [Authorize] attribute will be validated with JWT
    var audiences = DatabaseAccessLayer.GetAllowedAudiences(); // Gets a list of audience Ids, secrets, and names (although names are unused)

    // List the 
    List<string> audienceId = new List<string>();
    List<IIssuerSecurityTokenProvider> providers = new List<IIssuerSecurityTokenProvider>();
    foreach (var aud in audiences) {
        audienceId.Add(aud.ClientId);
        providers.Add(new SymmetricKeyIssuerSecurityTokenProvider(issuer, TextEncodings.Base64Url.Decode(aud.ClientSecret)));
    }

    app.UseJwtBearerAuthentication(
        new JwtBearerAuthenticationOptions
        {
            AuthenticationMode = AuthenticationMode.Active,
            AllowedAudiences = audienceId.ToArray(),
            IssuerSecurityTokenProviders = providers.ToArray(),
            Provider = new OAuthBearerAuthenticationProvider
            {
                OnValidateIdentity = context =>
                {
                    context.Ticket.Identity.AddClaim(new System.Security.Claims.Claim("newCustomClaim", "newValue"));
                    return Task.FromResult<object>(null);
                }
            }
        });
}