Non-paddy cropping systems play a significant role in food production. However, excessive nitrogen loss from non-paddy soils through nitrate leaching and ammonia volatilization poses a significant challenge to environmental sustainability. In this study, microcosm and field-scale experiments were conducted to explore the potential for using hydrogen peroxide (H2O2) to mitigate nitrogen loss and greenhouse gas emissions, aiming at filling gaps in knowledge regarding the underlying biochemical mechanisms. The results show that input of micromolar H2O2 from either artificial addition or natural rainwater into soils in the presence of magnetite (Fe3O4) could trigger Fenton-like reaction, which inhibited microbially mediated nitrification of soil-borne ammonium but did not affect the growth of the test crop plant (water spinach). In the absence of Fe3O4, input of rainwater-borne H2O2 into non-paddy soils caused reduction in the emissions of nitrous oxide (N2O) and carbon dioxide (CO2). There was a trend showing that the degree of reduction in N2O and CO2 fluxes increased with increasing concentration of rainwater-borne H2O2. It was likely that microbially mediated reduction of iron oxides took place during rainfall events, providing Fe(II) that is needed for reaction with rainwater-borne H2O2, triggering Fenton-like reaction to inhibit the soil microbes that mediate production of N2O and CO2 in the soils. The findings obtained from this study have implications for developing strategies to manage soil‑nitrogen to minimize its environmental impacts.