Young animals such as calves may be fed milk replacers containing soy having been preserved through treatment with acid-producing bacteria that reduces a pH of the milk replacer through microbial digestion of sugars present in soy to thereby produce a fermented milk replacer. The milk replacer is edible for at least 48 hours and its digestibility in the young animals is increased due to the microbial digestion of sugars in the soy that are otherwise indigestible in the gut of the young animals. The fermented milk replacers may be ingested by young animals in group settings. In addition, the milk replacers containing soy may be treated with enzymes adapted to hydrolyze complex indigestible carbohydrates within the milk replacer, potassium sorbate or both. Feeding systems incorporating these fermented milk replacers may result in increased gain and increased dry matter intake without negatively affecting animal health.