Environmentally persistent free radicals (EPFRs) are often generated during biochar production, but their toxicity on soil bacteria is still not truly reflected when considering the real soil condition. Herein, we detected the free radicals contents in biochar-spiked soil, and investigated soil bacterial responses to free radicals from the perspectives of enzyme activities, community structure, and ecoenzymatic stoichiometry. Biochar addition definitely enhanced the contents of EPFRs and its derived hydroxyl radicals (·OH) in the soil to the maximum values of 12.96 ± 0.47*1017 and 3.47 ± 0.13*1013 spin g-1, respectively. The increased EPFRs and ·OH broke nutrient balance by promoting the release of dissolved organic carbon and ammonium nitrogen (r2 = 0.886-0.984, P < 0.05) in soil, thus aggravating P limitation. This was further confirmed by increased alkaline phosphatase activity from 702 ± 24.5 to 874 ± 9.75 nmol g-1 h-1. The P limitation induced by EPFRs and ·OH indirectly decreased bacterial alpha diversity, as evidenced by the negative correlation between P limitation and bacterial alpha diversity (r2 = -0.931--0.979, P < 0.01) and structural equation model. Our study indicates that in addition to the previously reported direct toxicity, there is a new mechanism that free radicals indirectly reduced bacterial diversity by aggravating P limitation. These findings provide a novel perception to assess the eco-toxicity of biochar-associated free radicals.