AbstractAqueous proton batteries are promising candidates for the harvest and utilization of renewable yet intermittent energies. The redox couple of MnO₂/Mn²⁺ is one of the most competitive cathodes to enable proton batteries with high voltage. However, electrolytic products of the MnO₂/Mn²⁺ reactions tend to disperse into acidic electrolytes, and the composition of the electrolytic products as well as their influences on the counter electrode and the overall batteries are still unclear. Herein, the behaviors of the manganese electrolysis are studied with electrolytes of different proton concentrations and under variant current densities. The electrolytic products are disclosed to be ɛ‐MnO₂ regardless of the acidities of electrolytes and report, for the first time, the dispersed MnO₂ can chemically oxidize or dissolve the anode materials and subsequently induce self‐discharging. A membrane‐assisted protection strategy is proposed to prevent the free‐shuttle of MnO₂ particles and mitigate the battery self‐discharging. Accordingly, a much‐enhanced shelf‐life performance (61.3% capacity retention over a one‐week rest) is achieved for pyrene‐4,5,9,10‐tetraone//MnO₂ full‐cell. Furthermore, a customized device is developed with Nafion membrane, reaching excellent cycling stability (3000 cycles, 54 days) and a low self‐discharging rate. The findings and strategies for mitigating the self‐discharging issues are anticipated to advance the MnO₂/Mn²⁺‐based aqueous batteries and beyond.