The functional properties (protein solubility, emulsification characteristics, foaming characteristics, water- and fat-binding capacities) of extruded-expelled (EE) soy flours originating from six varieties of value-enhanced soybeans (high-sucrose, high-cysteine, low-linolenic, low-saturated FA, high-oleic, and lipoxygenase-null) and two commodity soybeans were determined. The soy flours varied in protein dispersibility index (PDI) and residual oil (RO), with PDI values ranging from 32 to 50% and RO values ranging from 7.0 to 11.7%. Protein solubility was reduced at pH values near the isoelectric region and was higher at both low and high pH. There were no significant differences for water-holding capacity, fat-binding capacity, emulsification activity, or emulsification stability. Only the high-oleic soy flour had significantly lower emulsification capacity. In general, the PDI and RO values of EE soy flours originating from value-enhanced and commodity soybeans had the greatest influence on protein functionality. The genetic modifications largely did not affect functional properties.