Manganese oxide nanostructures are synthesized by a route inspired by microbial mineralization in nature. The combination of organic molecules, which include antioxidizing and chelating agents, facilitates the parallel control of oxidation states and morphologies in an aqueous solution at room temperature. Divalent manganese hydroxide (Mn(OH)2) is selectively obtained as a stable dried powder by using a combination of ascorbic acid as an antioxidizing agent and other organic molecules with the ability to chelate to manganese ions. The topotactic oxidation of the resultant Mn(OH)2 leads to the selective formation of trivalent manganese oxyhydroxide (β-MnOOH) and trivalent/tetravalent sodium manganese oxide (birnessite, Na0.55Mn2O4·1.5H2O). For microbial mineralization in nature, similar synthetic routes via intermediates have been proposed in earlier works. Therefore, these synthetic routes, which include in the present study the parallel control over oxidation states and morphologies of manganese oxides, can be regarded as new biomimetic routes for synthesis of transition metal oxide nanostructures. As a potential application, it is demonstrated that the resultant β-MnOOH nanostructures perform as a cathode material for lithium ion batteries.