Processes for separating and isolating proteins and fats from biomass matter utilizes a pH adjustment of a slurry. The biomass feedstock is derived from commingled animal and/or plant-based streams with highly variable concentrations of fat, proteins and impurities present in the biomass. A wide range of pH adjustment spanning highly acid to highly basic has been shown to be effective at separating the commingled streams into their constituent products. The processes do not rely on the proteins being solubilized into the solution, but rather solubilizing the fat portion, physically separating the constituents and precipitating the fat in a downstream process, resulting in two value streams: a highly digestible protein component and a fat component. The protein component has nutritional value as companion pet, animal and aquaculture feed ingredient and the fat component has value as standalone or blended solid or liquid biofuels, greases or specialty chemicals.