Although this highly depends on the alternatives used, we can give you a general idea of the calorie count of a sugar-free vanilla cupcake. It roughly contains 32.5 calories per cupcake, out of which 14 come from the almond meal or any alternative flour used. The rest of these come from eggs and either milk or yogurt, whichever is used. If you use a frosting with heavy cream, it will add to the count.