Industrial-scale filter dryers, equipped with one or more microwave input ports, have been modelled with the aim of detecting existing criticalities, proposing possible solutions and optimizing the overall system efficiency and treatment homogeneity. Three different loading conditions have been simulated, namely the empty applicator, the applicator partially loaded by both a high-loss and low loss load whose dielectric properties correspond to the one measured on real products. Modeling results allowed for the implementation of improvements to the original design such as the insertion of a wave guide transition and a properly designed pressure window, modification of the microwave inlet's position and orientation, alteration of the nozzles' geometry and distribution, and changing of the cleaning metallic torus dimensions and position. Experimental testing on representative loads, as well as in production sites, allowed for the confirmation of the validity of the implemented improvements, thus showing how numerical simulation can assist the designer in removing critical features and improving equipment performances when moving from conventional heating to hybrid microwave-assisted processing.