A fuzzy multiple-input-multiple-output (MIMO) control algorithm was developed and applied to control a non-isothermal continuous crystallizer. The algorithm included two feedback control loops and two decouplers. The first loop controls the crystallizer temperature manipulating the cooling water flow rate, and the second loop controls the crystal size distribution mean manipulating the agitation rate. Fuzzy controllers and decouplers were trained using open loop simulated information. The fuzzy algorithm was compared to a MIMO conventional PID control system measuring the integral of square error (ISE) and the integral of the absolute value error (IAE) when temperature and crystal size distribution mean set points changed. In addition, disturbances caused by changes in the cooling water temperature were analyzed. Fuzzy and conventional controllers were tuned by minimizing the ISE using the nonlinear least-squares Matlab algorithm (lsqnonlin). The results showed that the fuzzy control algorithm could be successfully used to control a non-isothermal continuous crystallizer.