If you’re using the DI container to manage the DbContext (i.e. you’re adding the DbContext to the service collection), the command timeout can be specified in the options.
In Startup.ConfigureServices:
services.AddDbContext<YourDbContext>(options => options.UseSqlServer(
this.Configuration.GetConnectionString("YourConnectionString"),
sqlServerOptions => sqlServerOptions.CommandTimeout(60))
);