The problem of process control in the field of pharmaceutical freeze drying is discussed, and a model predictive control (MPC) system is proposed to control, and optimize, in-line the primary drying step, beside preserving product quality. The controller can provide the optimal recipe for a given product, taking into account process constraints and modeling errors. Two control algorithms are proposed: the former manipulates both the chamber pressure and the temperature of the technical fluid, while the latter manipulates only the temperature of the fluid. The optimal formulation of the algorithms and the tuning of controller parameters are discussed by means of mathematical simulations.