Constipation is not a side effect associated with soy formula. Soy formula is a treatment for constipation in infants. The National Institute of Health classifies soy infant formula as a substance of minimal concern in regard to side effects.

In addition to its use for constipation, soy formula is prescribed to infants with milk allergies. Three percent of infants in the United States have milk allergies, and most eventually outgrow them. Soy milk is the most common treatment for this allergy, and it is nutritionally equivalent to cow's milk formula. Soy formula comprises 12 percent of all formula sales in the United States as of 2014, which is a 50 percent decrease in sales from its peak in 1999.

The only documented side effect of soy formula in humans is the effect it has on those with a soy allergy. Animal studies show a correlation between high soy intake and early puberty due to increased levels of estrogen, but this finding is not confirmed in humans. The National Institute of Health and the U.S. Department of Agriculture both cite long-term studies as evidence that soy formula is a safe alternative to cow's milk formula though both agencies encourage parents to feed infants breast milk instead of formula whenever possible.