Soil biosolarization (SBS) is a pest control technique that combines passive solar heating and fermentation of amended organic matter. The extreme soil conditions generated during SBS could decrease microbial biomass and restructure the soil microbiome, which could impact soil quality. Digestates from anaerobic digesters may harbor microbial communities tolerant of the oxygen, moisture, and temperature stresses encountered during SBS as these conditions may also occur in digesters. Digestate microbial communities may contribute to soil fermentation during SBS and affect organic matter turnover in soils treated with SBS. The objective of this study was to assess the effect of SBS on soil microbial diversity and quantity when solid digestates from thermophilic (TD) and mesophilic (MD) anaerobic digesters were used as soil amendments. In the soils amended with TD, communities showed the greatest divergence from the initial soil state whereas MD amendment resulted in a microbiome more similar to the non-amended soil. The microbial biomass of the biosolarized soils was significantly greater than the non-amended, solar-heated soil. The microbial biomass in the biosolarized soils was dominated by K-strategic or “native” species. Solar heating of the non-amended soil mainly affected “native” species, leading to conditions where other opportunistic species become more dominant. Further studies are needed to elucidate whether the persistent microbes in the soil are benign or pathogenic and to understand their roles in pest inactivation and nutrient cycling during and following SBS.