Developing high-performance aqueous Zn-ion batteries from sustainable biomass becomes increasingly vital for large-scale energy storage in the foreseeable future. Therefore, γ-MnO2 uniformly loaded on N-doped carbon derived from grapefruit peel is successfully fabricated in this work, and particularly the composite cathode with carbon carrier quality percentage of 20 wt% delivers the specific capacity of 391.2 mAh g-1 at 0.1 A g-1, outstanding cyclic stability of 92.17% after 3000 cycles at 5 A g-1, and remarkable energy density of 553.12 Wh kg-1 together with superior coulombic efficiency of ~ 100%. Additionally, the cathodic biosafety is further explored specifically through in vitro cell toxicity experiments, which verifies its tremendous potential in the application of clinical medicine. Besides, Zinc ion energy storage mechanism of the cathode is mainly discussed from the aspects of Jahn–Teller effect and Mn domains distribution combined with theoretical analysis and experimental data. Thus, a novel perspective of the conversion from biomass waste to biocompatible Mn-based cathode is successfully developed.