Abstract: Alkaline extraction followed by acid precipitation or ultrafiltration method for preparation of protein isolates from oilseeds cakes/meals is followed. The strong alkaline and acidic conditions alter the functional properties of the protein, which adversely affects its quality. The present invention provides a microbial based process to produce protein isolates/concentrates from oilseed cakes/meals or from other similar type of sources either plant or animal origin without addition of strong or diluted acid. The protein is extracted in aqueous media or alkaline aqueous media with or without containing specified salt for specified duration. The extract is centrifuged, mixed with known microbial culture (the process is not limited to the particular strain) and incubated at particular temperature and duration. The precipitated protein is recovered and dried to get protein isolates/concentrates.