Methylmercury formation is the major concern of global mercury contamination. Accurate prediction of methylmercury production remains elusive due in part to the lack of mechanistic understanding of microbial methylation potential of particulate-phase mercury. Here we show that the methylation potential of nanoparticulate metacinnabar, which is formed during the early stage of mercury mineralization and is ubiquitous in contaminated soils and sediments, is determined by its exposed facets. Nanoparticulate metacinnabar with higher (111) content exhibits significantly greater affinity to the methylating bacterium Desulfovibrio desulfuricans ND132, leading to higher methylmercury production. This is likely attributable to the favored binding between the (111) facet and the protein transporter responsible for mercury cellular uptake prior to methylation. The (111) facet of metacinnabar tends to diminish during nanocrystal growth, but natural ligands alleviate this process by preferentially adsorbing to the (111) facet (verified with adsorption experiments using facet-engineered model materials coupled with theoretical calculations). This facet evolution of metacinnabar and its subsequent effect on mercury bioavailability explain the intriguing observation that methylation potential of nanoparticulate mercury is surface-area-independent. Our discovery provides new mechanistic insights for interfacial processes involved in nanoparticle−microorganism interactions that have important implications for understanding the environmental behavior of mercury and other nutrient or toxic elements associated with widely present crystalline nanoparticles.