Disclosed are calcium fortified, soy-based, infant nutritional formulas, including powder, liquid, or concentrate embodiments comprising per 100 kcal of formula (A) lipid, preferably up to about 8.0 g, (B) carbohydrate, preferably from about 8.0 g to about 16.0 g, (C) phytase-treated soy protein, preferably up to about 3.5 g and (D) calcium, preferably up to about 90 mg of calcium; wherein the nutritional formula is an infant formula having a calcium to lipid weight ratio of from about 0.002 to about 0.020, and wherein the formula contains not more than about 8.4 mg phytic acid per 100 kcal of formula. It has been found that these calcium-fortified, phytase-treated, soy-based, nutritional formulas provide for softer stools in infant populations, especially as compared to infants fed with other soy-based formulas including commercial soy formulas as well as soy based formulas derived from dephytinization methods other than phytase treatment, e.g., ion exchange.