I have an ASP.NET Core MVC application that also hosts an API. The site uses Identity defaults so when you log in a cookie is set. The API has been configured to use JWT Beare
You should be able to configure the cookie path in ConfigureServices
like:
services.ConfigureApplicationCookie(options =>
{
options.Cookie.Path = "/";
});
See https://docs.microsoft.com/en-us/aspnet/core/security/authentication/identity-configuration?view=aspnetcore-2.1&tabs=aspnetcore2x#cookie-settings