Phyllomanganates of the birnessite family are the most abundant manganese oxides on Earth and the strongest inorganic oxidants in the environment. Birnessite controls the oxidative scavenging of cobalt in soils, lake and marine sediments, and ferromanganese crusts and nodules, leading to enrichments of the order of one billion times the concentration in solution. However, a detailed mechanistic understanding of the enrichment processes is lacking. Here, we perform density functional theory (DFT) calculations to explore the mechanisms of Co(II) to Co(III) oxidation on the layer edge and surface of birnessite nanoparticles. We show that Co(II) sorption on a layer edge is an unlikely oxidation pathway. In contrast, Co(II) sorbed on a Mn(IV) vacancy site exposed on the layer surface as an octahedral triple-corner sharing (TCS) complex enters the vacancy where it is oxidized to Co(III) by a layer Mn(IV) cation, which is reduced to Mn(III). The stepwise reaction proceeds as follows. The octahedral TCS complex is transformed to a smaller tetrahedral TCS complex, allowing Co(II) to cross the surface oxygen layer and to fill the empty octahedral Mn(IV) site. When in the octahedral vacancy, Co(II) is converted from the high-spin (t2g 5 eg 2) to the low-spin (t2g 6 eg 1) state and the Co(II) octahedron becomes strongly distorted by the Jahn-Teller effect. Afterward, the electron exchange reaction between Mn(IV) (t2g 3 eg 0) and Co(II) (t2g 6 eg 1) takes place, resulting in the formation of a regular lowspin Co(III) (t2g 6 eg 0) octahedron and a Jahn-Teller distorted high-spin Mn(III) (t2g 3 eg 1) octahedron. These findings refine previously proposed mechanisms of Co(II) oxidation by birnessite and fill gaps in our understanding of global Co sequestration in natural systems.