In this work, we show the development of a numerical model to investigate the 3D interactions between microwave radiation and basalt, granite, and sandstone rock samples. In particular, we assign sample heterogeneity based on the Weibull statistical distribution, and invoke a damage model for elemental tensile and compressive stresses based on the maximum tensile stress and the Mohr–Coulomb theories, respectively. Model implementation is facilitated by the use of comsol for use in coupling the electromagnetic, thermal, and solid displacement relations. Various parametric studies are conducted related to variable input power and waveguide port alignment, with model validation conducted with respect to damage resulting from a uniaxial compression test. The results indicate that relatively high induced temperatures will promote damage potential, but its impact must be placed within the context of the sample strength to quantify the true potential damage evolution of a given rock mass. As observed herein, a mechanically weaker rock may be prone to mechanical damage; however, it may also possess a relatively large relative permittivity, enabling it to absorb the least amount of microwave radiation thus yielding comparatively low overall damage profiles compared to a more mechanically competent rock mass.