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Electrochemical activation techniques and the use of multi-shell structured materials are effective strategies to enhance the electrochemical performance of rechargeable aqueous zinc-ion capacitors (ZICs). In this study, we successfully synthesized spherical Ni3Mn-MOFs via a solvothermal method and used them as templates to prepare Ni/MnO@C nanospheres with different core–shell structures by adjusting the heating rate under an Ar atmosphere. The multi-shelled structure provides more active sites and alleviates structural strain associated with repeated Zn2+ insertion/extraction processes. During the initial charge process, the Ni/MnO@C cathode undergoes electrochemical activation and generates oxygen vacancies, which can facilitate Zn2+ adsorption and promote ion diffusion, significantly enhancing its initial capacity and cycling stability. The activated Ni/MnO@C electrode exhibits an excellent capacity of 500 mA h g−1 at a current density of 0.3 A g−1, and the capacity retention rate remains as high as 90.9% even after 5200 cycles at 3 A g−1. The assembled AC//Ni/MnO@C (AC: active carbon) ZIC demonstrates an energy density of 90.14 W h kg−1 at a power density of 2750.17 W kg−1. At 3 A g−1, the capacity retention rate remains as high as 80.3% after 6000 cycles, indicating excellent long-term durability. This work provides a promising strategy for designing high-performance cathodes for the next generation of ZICs. [ABSTRACT FROM AUTHOR]