Despite its presence in limited amounts, birnessite has a wide spread distribution and is often highly enriched in trace metals such as Co in diverse geological environments. This study investigated the effects of Co doping on the layer structure and properties of birnessites synthesized through the oxidation of Mn2 + by O2 under alkaline conditions, by using powder X-ray diffraction (XRD) and X-ray absorption spectroscopy (both XANES and EXAFS). The Co doped, high-pH birnessites are composed of platy crystals, and have lower crystallinity, larger specific surface areas (SSAs) and higher Mn average oxidation states (AOSs) than pure birnessite. Cobalt K-edge EXAFS analysis reveals that no CoOOH is formed, and ~ 76% of the total Co is located in the layers of the Co-doped birnessites. Careful examination of these Co-doped samples by XRD and EXAFS analyses demonstrates that the presence of Co during the synthesis of high-pH birnessite promotes the structural transition of the birnessite layer symmetry from orthogonal to hexagonal. This is due to the decrease in Mn(III) in the layers of the doped solids, leading to the attenuation of Jahn–Teller effect. The decrease in Mn(III) in the layers might be attributed to the substitution of Mn(III) by Co(III) in the layers. The competitive adsorption of Co2 +/3 + with Mn2 + might also decrease the oxidation of Mn2 + to Mn(III) and the subsequent migration of Mn(III) into the birnessite layers. The results provide new insights into the interaction mechanisms between transition metals and birnessite-like minerals, and improve our understanding of the abiotic oxidation of Mn2 + as well as the prevalence of birnessites with hexagonal symmetry in natural environments.