Single-atom nanozymes (SAzymes) offer exceptional promise as next-generation substitutes for natural enzymes due to its superior catalytic performance. However, single active sites of SAzymes have predominantly been limited to mimicking a monofunctional enzymatic activity, which hinders their adaptability in complex biological systems. Herein, an innovative Ce-induced adaptive synergism is reported, which allows Ce single-atom to activate Ni-Fe dual-site adaptive synergy for boosting multi-enzymatic activities of Ce-modified nanozyme (Ce-MOF), along with finely tuned reactive oxygen species (ROS) production. In-situ spectroscopic studies and theoretical calculations reveal that Ce induces spin-state polarization of Ni and Fe centers, promoting the generation of bound Ni/Fe = O intermediates that modulate ROS pathways depending on substrate and pH. This adaptive synergism enables continuous structural adaptation of the dual-metal active sites, enhancing both catalytic efficiency and selectivity. Functionally, Ce-MOF exhibits potent antifungal activity against Fusarium solani in vitro without the introduction of exogenous O2 or H2O2. Meanwhile, soil experiments demonstrate effective inhibition of phytopathogen colonization and a notable recovery of beneficial microbial communities via selective production of ROS. Furthermore, the amended soil treated with Ce-MOF flourishes Panax ginseng growth and provides a promising solution for sustainable plant cultivation via rhizosphere microbiome regulation.