Increasingly, extruding-expelling (E-E) plants, often referred as “mini-mills,” are being constructed by farmer-owned businesses to process soybeans produced in local areas. E-E processing is a mechanical process that has several advantages over conventional processing methods. E-E mills, most employing the Express System® (Insta-Pro Div., Triple “F”, Inc., Des Moines, IA), are relatively small, with capacities ranging from 6 to 120 tons/day. They have low initial capital investment ($150,000–200,000) and relatively low operating costs ($25/ton) (1). E-E mills are especially well suited for processing identity-preserved (IP) soybeans. The largescale solvent extraction (SE) facilities, which have typical crushing capacities of 2,000 to 3,000 tons/day, are not feasible for flexible IP processing. Usually, there is low production tonnage during the developmental stages of these seeds, and a large number of value-added traits are being developed. Recent stringent environmental laws also often restrict construction of new SE plants, and E-E mills can be an alternative. Because E-E products are not treated with chemical solvents, the crude oil and meal may be considered to be “organic” or “natural,” if appropriate methods are used during soybean production and further processing. Currently, the partially defatted soybean flour (about 6% residual oil) produced from these operations is not extensively used in food applications due to limited technical information on protein functionality and on performance in food applications. Some of the potential applications include baking, meat extending, animal feeding, and producing industrial soy protein–based adhesives. This chapter summarizes the recent efforts aimed at improving E-E processing and developing applications for E-E protein products.