A system for modifying dairy protein functionality can include a milk protein input, a treatment process, and a milk protein output. A controller can be in communication with the treatment process and can be configured to receive one or more input parameters. The controller can generate one or more treatment parameters based on the one or more input parameters. The controller can then initiate the treatment process based on one or more of the treatment parameters. The modified dairy protein functionality can be selected or optimized based on a target functionality of the milk protein output.