human biology - Where does all the food go?

Whatever the diet, the food intake contains macronutrients: carbohydrate, fat and protein. When they are metabolised all of these molecules will end up, for the most part, as carbon dioxide, water, and ammonia, unless they are incorporated into components of the body.

These waste products are, of course, lost via breathing, and via the urine. That's where the "missing mass" goes.

A related question is here.