Aqueous zinc ion batteries (ZIBs) are emerging as a highly promising alternative technology for grid-scale applications where high safety, environmental-friendliness, and high specific capacities are needed. It remains a significant challenge, however, to develop a cathode with a high rate capability and long-term cycling stability. Here, we demonstrate diffusion-controlled behavior in the intercalation of zinc ions into highly porous, Mn4+-rich, and low-band-gap NixMn3−xO4 nano-particles with a carbon matrix formed in situ (with the composite denoted as NixMn3−xO4@C, x = 1), which exhibits superior rate capability (139.7 and 98.5 mA h g−1 at 50 and 1200 mA g−1, respectively) and outstanding cycling stability (128.8 mA h g−1 remaining at 400 mA g−1 after 850 cycles). Based on the obtained experimental results and density functional theory (DFT) calculations, cation-site Ni substitution combined with a sufficient doping concentration can decrease the band gap and effectively improve the electronic conductivity in the crystal. Furthermore, the amorphous carbon shell and highly porous Mn4+-rich structure lead to fast electron transport and short Zn2+ diffusion paths in a mild aqueous electrolyte. This study provides an example of a technique to optimize cathode materials for high-performance rechargeable ZIBs and design advanced intercalation-type materials for other energy storage devices.