A method includes receiving a measurement associated with a cloud point of a biofuel being produced in a refining system. The method also includes determining how to adjust the refining system based on a desired cloud point of the biofuel and the measurement associated with the cloud point. The method further includes outputting a control signal to adjust the refining system based on the determination. Determining how to adjust the refining system could include determining how to adjust an inlet temperature of a reactor in the refining system. The reactor could represent an isomerization reactor, and a heater could heat material entering the isomerization reactor. Determining how to adjust the inlet temperature of the reactor could include determining how to adjust operation of the heater. A model predictive control (MPC) technique could be used to determine how to adjust the inlet temperature of the isomerization reactor.