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Manganese oxide materials are attracting considerable interest for clean energy storage applications such as rechargeable Li ion and Li–air batteries and electrochemical capacitors. The electrochemical behavior of nanostructured mesoporous β-MnO2 is in sharp constrast to the bulk crystalline system, which can intercalate little or no lithium; this is not fully understood on the atomic scale. Here, the electrochemical properties of β-MnO2 are investigated using density functional theory with Hubbard U corrections (DFT+U). We find good agreement between the measured experimental voltage, 3.0 V, and our calculated value of 3.2 V. We consider the pathways for lithium migration and find a small barrier of 0.17 eV for bulk β-MnO2, which is likely to contribute to its good performance as a lithium intercalation cathode in the mesoporous form. However, by explicit calculation of surface to bulk ion migration, we find a higher barrier of >0.6 eV for lithium insertion at the (101) surface that dominates the equilibrium morphology. This is likely to limit the practical use of bulk samples, and demonstrates the quantitative importance of surface to bulk ion migration in Li ion cathodes and supercapacitors. On the basis of the calculation of the electrostatic potential near the surface, we propose an efficient method to screen systems for the importance of surface migration effects. Such insight is valuable for the future optimization of manganese oxide nanomaterials for energy storage devices.