Freeze-drying is a common process to extend the shelf life of food and bioactive substances. Its main drawback is the long drying time and associated high production costs. Microwaves can be applied to significantly shorten the process. This study investigates the effects of modulating the electromagnetic field in microwave-assisted freeze-drying (MFD). Control concepts based on microwave frequency are evaluated using electromagnetic simulations. The concepts are then applied to the first part of primary drying in a laboratory-scale system with solid-state generators. Targeted frequency modulation in the electromagnetic simulations enabled an increase in energy efficiency or heating homogeneity throughout MFD while having negligible effects on the power dissipation ratio between frozen and dried product areas. The simulations predicted the qualitative effects observed in the experimental proof of concept regarding energy efficiency and drying homogeneity. Additionally, shortened drying times were observed in the experiments with a targeted application of energy-efficient frequencies. However, differences occurred in the quantitative validation of the electromagnetic models for energy efficiency in dependence on frequency. Nevertheless, the models can be used for a time-efficient investigation of the qualitative effects of the control concepts. In summary, frequency-based control of MFD represents a promising approach for process control and intensification.