For over three centuries, soil scientists and microbiologists have been studying the most diverse habitat on the planet, characterizing the structure, function, and composition of the soil microbial community through a diverse array of techniques. Yet our understanding of the soil microbiome and the reciprocal dynamics with metal speciation and bioavailability remain primarily limited to model systems and isolated organisms. Metals, however, are ubiquitous in the environment, pervasive in agriculture, and essential to life functions. The purpose of this chapter is to review our existing knowledge on the soil factors that control metal bioavailability and bring that knowledge together with our understanding of dynamics of metals and metalloids with microbial communities in soil to highlight the current gaps in metal-microbiome research. Ultimately, restoration of ecosystem function, enhanced soil health and quality, and any type of management for microbial metal transformations will only be possible with a thorough understanding of how soil microbiomes interact with each other, the soil, their associated plant communities, and the impacts these interactions have on the molecular details underlying their biogeochemical function.