Printed flexible energy storage devices such as micro-supercapacitors require high electrochemical performance for practical applications. Here, we report a high volumetric energy density of up to 1.13 × 10−3 Wh cm−3 at a power density of 0.11 W cm−3 by inkjet printing of Fe-doped MnO2 nanosheets inks as active materials on polyimide substrates. The enhancement results from atomic-level substitutional doping of 3d metal ions (Co, Fe, Ni) in sub-nanometer thick 2D MnO2 nanosheets. Substitutional doping introduces new electronic states near the Fermi level, thereby enhancing the electronic conductivity and contributing to the formation of redox-active 3d surface states. Fe-doped MnO2 showed the best performance in terms of specific areal and volumetric capacitance. Our finding suggests that the rational doping at atomic scale shows great promise for achieving high energy and power density flexible energy storage devices.