Solar‐driven biohybrid systems that produce chemical energy are a valuable objective in ongoing research. However, reactive oxygen species (ROS) that accompany nanoparticle production under light radiation severely affect the efficiency of biohybrid systems. In this study, we successfully constructed a two‐hybrid system, Shewanella oneidensis‐CdS and S. oneidensis‐CdS@Fe3O4, in a simple, economical, and gentle manner. With the Fe3O4 coating, ROS were considerably eliminated; the hydroxyl radical, superoxide radical, and hydrogen peroxide contents were reduced by 66.7%, 65.4%, and 72%, respectively, during light‐driven S. oneidensis‐CdS hydrogen production. Shewanella oneidensis‐CdS@Fe3O4 showed a 2.6‐fold higher hydrogen production (70 h) than S. oneidensis‐CdS. Moreover, the S. oneidensis‐CdS system produced an additional 367.8 μmol g‐dcw−1 (70 h) of hydrogen compared with S. oneidensis during irradiation. The apparent quantum efficiencies of S. oneidensis‐CdS and S. oneidensis‐CdS@Fe3O4 were 6.2% and 11.5%, respectively, exceeding values previously reported. In conclusion, a stable nanozyme coating effectively inhibited the cytotoxicity of CdS nanoparticles, providing an excellent production environment for bacteria. This study provides a rational strategy for protecting biohybrid systems from ROS toxicity and contributes to more efficient solar energy conversion in the future.This article is protected by copyright. All rights reserved