Biogenic Mn-oxides (BioMnO(x)), produced by microorganisms, possess an extraordinary ability to sequester metals. BioMnO(x) are generally layered structures containing varying amounts of Mn(III) and vacant sites in the Mn layers. However the relationship between the varying structure of BioMnO(x) and metal sorption properties remains unclear. In this study, BioMnO(x) produced by Pseudomonas putida strain GB-1 was synthesized at either pH 6, 7, or 8 in CaCl(2) solution, and Ni(II) sorption mechanisms were determined at pH 7 and at different Ni(II) loadings, using isotherm and extended X-ray absorption fine structure (EXAFS) spectroscopic analyses. Our data demonstrate that Ni(II) sorbs at vacant sites in the interlayer of the BioMnO(x) and the maximum Ni(II) sorption capacity increases as the formation pH of BioMnO(x) decreases. This relation indicates that the quantity of BioMnO(x) vacant sites increases as formation conditions become more acidic, which is in good agreement with our companion study. Contents of the vacant sites were quantitatively estimated based on maximum Ni(II) sorption capacity. Additionally, this study reveals that imidazole groups are involved in Ni(II) binding to biomaterials, and have a higher Ni(II) sorption affinity, but a lower site density compared to carboxyl groups.