Prokaryotes, including bacteria, are a major component of both modern and ancient ecosystems. Although fossilized prokaryotes are commonly discovered in sedimentary rocks, it is rare to find them preserved in situ alongside macrofossils, particularly as pyritized cells in sites of exceptional fossil preservation. We examined prokaryotes preserved in the Lower Cretaceous Crato Formation of Brazil and demonstrate the widespread presence of spherical microorganisms preserved on the surface of Crato invertebrate fossils. These microorganisms were pyritized, covering decaying carcasses, 1.14 ± 0.01 μm in size, hollow with smooth surfaces, and can be found as aggregates resembling modern prokaryotes, particularly, coccoid bacterial colonies. It is likely that the observed microorganisms covered the carcasses before permissive conditions were established for pyritization, which must have been so rapid as to inhibit the autolysis of their delicate membranes. This is a new record of prokaryote fossils preserved in pyrite in association with macrofossils, which highlights the unique diagenetic and paleoenvironmental conditions of the Crato Formation that facilitated this mode of fossilization.