This invention relates to a process for manufacturing nutritionally balanced food compositions suitable for retort sterilization which have a low pH, extended shelf life, high antimicrobial activity, and which include protein in a stable emulsion. The primary protein source for the food composition is caseinates or milk protein concentrates and isolates comprised mostly of casein. Alternately, milk protein concentrates, milk protein isolates, milk protein hydrolystates, soy protein isolates or soy protein concentrates may also be used. The process includes two homogenization steps.