Intensive agriculture results in soil degradation, especially with the depletion of soil organic carbon (SOC). Application of organic fertilizers (e.g., animal manures) alone or combined with chemical fertilizers can alleviate soil degradation by increasing soil C while causing variations in soil hydrogen peroxide (H 2 O 2 ) and iron availability.However, the underlying relationships among soil H 2 O 2 production, iron availability, and soil C storage following organic fertilization remain poorly understood. By combining results from three agroecosystem experiments from temperate northern to subtropical southern China with 25-29 years of different fertilization treatments (no fertilization, Control; inorganic nitrogen, phosphorus and potassium fertilization [NPK]; NPK plus manure [NPKM]), here, we show that NPK treatments increased soil H 2 O 2 but decreased biodiversity (i.e., Shannon index) and SOC compared with NPKM treatments across all of the three experiments. In all of the examined soils, the contents of H 2 O 2 were approximately 0.7-to 7-fold higher under NPK treatment than under Control or NPKM treatments. The contents of H 2 O 2 were significantly affected by the fertilization regimes, experimental places, and their interaction. Compared with Control and NPKM treatments, NPK treatment decreased Shannon index to the greatest extent (~1.5) at the Qiyang experiment in subtropical southern China, followed by Jinxian (~0.6) in subtropical southern China, and Gongzhuling (~0.3) in temperate northern China. There was a significant and negative correlation between soil H 2 O 2 and Shannon index or mobilized iron, indicating that high biodiversity and high mobilized iron were beneficial to the decay of soil H 2 O 2 . Results from microcosm experiments support the field observations, implying that the occurrence of microbial-mediated Fenton-like reactions or free radical reactions was influenced by organic inputs. Together, these findings suggest that long-term manure inputs to soil initialize free radical reactions by activating microbial communities and mobilizing iron, providing benefits for soil C stabilization and storage by increasing recalcitrance and SOC interactions.