The coupling of environmental remediation and advanced material preparation through plant cells, also called bioreactors, is of great significance for achieving the waste valorization of pollutants. However, elucidating the intricate interactions among metal ions within bioreactors and subsequent products remains a critical challenge. Herein, a strategy of bimetallic synergistic metabolism utilizing Lemna cells to construct phase-controllable carbon-based composites for the anode of Li-ion batteries has been proposed. By systematically tuning the ratio of Fe3+ to Co2+/Ni2+ in simulated wastewater, the modulation of inorganic phase composition within derived-carbon can be achieved. The competitive allocation of phosphate ions by distinct metal species within bioreactors serves as a pivotal factor governing the phase evolution of metal precursors. Sulfurization effectively converts adjacent metal compounds into bimetallic sulfides. Owing to the engineered bimetallic synergy and phase architecture, the resulting composites exhibit superior “fast-charging” performance, among which the capacity of Lm-FeNi11-S remains almost unchanged (∼230 mAh g−1) after 1600 cycles at a current density of 1 A g−1, and still maintains a specific capacity of 185 mAh g−1 at a high current density of 10 A g−1. This work underscores the potential of this biometabolic pathway for converting hazardous wastewater streams into high-value energy storage materials.