The main purpose of this work was to extract valuable metals from EAF dust with the addition of biochar, using microwaves to control and optimize the carbothermical reduction process. To achieve better microwave penetration and the most homogeneous electromagnetic heat source distribution possible in a sample, the content of EAF dust and biochar in centimeter-size spherical particles prepared by the pelletization process was considered to be radially heterogeneous. The content of EAF dust was determined experimentally and the effective permittivity, permeability, and thermal conductivity of the EAF dust as well as biochar–EAF powder mixture were determined using effective medium approximation. The microwave heating of a multilayered pellet of biochar-containing EAF dust was simulated and investigated. The influence of the distribution of the components within the pellet on the effectiveness of the microwave heating was investigated, as was the influence of the biochar conductivity. The interaction of the pellet with both plane waves in free space and with H10 mode waves in a single-mode waveguide was considered. The most optimal distribution of EAF dust and biochar within the pellet for the reduction process was determined.