Soy formula has no nutritional advantage over milk-based formula and vice versa.
Both are fortified with the same vitamins and minerals. Babies can be chronically sensitive to cow's milk protein and may have to avoid it for the first several months of life. If your baby cries or is irritable during feedings or immediately afterward, or if he has diarrhea, he may be allergic to his formula. That said, remember that soy protein is just as likely to cause food allergies. In fact, most babies who are allergic to cow's milk protein are also allergic to soy protein.