A system and method for optimizing a process for refining lignocellulosic granular matter such as wood chips use a predictive model including a simulation model based on relations involving a plurality of matter properties characterizing the matter such as moisture content, density, light reflection or granular matter size, refining process operating parameters such as transfer screw speed, dilution flow, hydraulic pressure, plate gaps, or retention delays, at least one output controlled to a target such as primary motor load or pulp freeness, and at least one uncontrolled output such as specific energy consumption, energy split, long fibers, fines and shives. An adaptor is fed with measured values of matter properties and measured values of controlled and uncontrolled outputs, to adapt the simulation model accordingly. An optimizer generates a value of the target according to a predetermined condition on a predicted uncontrolled output parameter and to one or more process constraints.