Well-preserved Mn-rich oncoids are described from late Paleoproterozoic (ca. 1.9 Ga) shallow-water manganese ores at the Bronkhorstfontein deposit in the Northern Province of South Africa. A close examination reveals obvious similarities of these ancient oncoids to modern biogenic oncoids in terms of internal structure and porosity. The occurrence of Mn in the oncoids suggests that Mn precipitation was biogenically controlled, providing the earliest textural evidence for microbially mediated Mn precipitation in the geologic record. The late Paleoproterozoic appearance of Mn-rich oncoids is not restricted to the occurrence described, but has been noted in at least three other sedimentary successions. Their appearance coincides with the formation of the first shallow-water Mn deposits, and the corresponding demise of deep-water Mn formations. This change in Mn metallogenesis is tentatively attributed to the depletion of the primary deep-ocean Mn reservoir in the late Paleoproterozoic. This environmental pressure may have forced Mn-oxidizing microorganisms to adapt to the shallow sedimentary environment that was more proximal to the Mn supply from continental runoff.