Hydrothermal processes are provided for preparing hybrid proteins containing altered SS/SH bonds, thereby yielding hybrid proteins having enhanced functional and/or nutritional properties. The processes involve initial homogenization of a protein-containing slurry containing at least two proteins, followed by high pressure steam treatment in a jet cooker (16) or similar device in order to heat shock and thereby alter the conformation of some of the proteins, followed by a holding period to allow the proteins to reform, whereupon the proteins are cooled. Plant and animal proteins may be processed, and the starting slurry can be pH-modified and/or supplemented with one or more additional ingredients (e.g., salts, phosphates, fatty acids, polysaccharides, alcohols, aromatic compounds). The hybrid proteins are useful as food ingredients (e.g., solubility, wetability, dispersibility, foaming, emulsification, viscosity, gelation or thickening agents).