Unreasonal application of biogas manure discharged from the biogas plants in livestock farms increased the environmental risk. In this study, a 5-year 8-season tomato-pepper rotating protected field experiment was conducted, and the effects of different applied proportions of biogas manures and chemical fertilizer (100% biogas manures, 3/5 biogas manures plus 2/5 chemical fertilizer, 2/5 biogas manures plus 3/5 chemical fertilizer, 3/5 biogas manures and unfertilized treatments) on vegetable yield and soil accumulation of nitrogen (N), phosphorus (P) and heavy metals were investigated, in order to support the possibility of biogas manure to replace chemical fertilizer. The results showed that there were no significant effects on vegetable yields under the treatments with 100% biogas manures, 3/5 biogas manures plus 2/5 chemical fertilizer, 2/5 biogas manures plus 3/5 chemical fertilizer treatments with the same N and potassium (K) input. No significant differences were observed in the N surplus and soil total N in 0-180 cm soil depth after 5-years experiment. However P surplus significantly increased with the applied proportion of biogas manures. The contents of Olsen-P and CaCl2-P in the surface soil layer (0-30 cm) reached 151 and 8.0 mg/kg in treatment with 100% biogas manures application, respectively, much higher than other treatments, which significantly exceeded environmental threshold. Compared with the treatment with 100% biogas manures application, reduced biogas wastes application (3/5 biogas wastes) significantly decreased the nitrate leaching risk and P surplus. Compared with unfertilized treatment, the contents of total Hg in surface soil layer (0-30 cm) and total As content in the soil layer (0-180 cm) slightly increased, whereas the contents of total Cr, Cd and Pb in soil decreased, especially Pb, in the treatments with biogas manures application. No heavy metal pollution risk was observed in all treatments. Biogas manure replacing chemical fertilizer can effectively achieve the waste recycling utilization, but increase the risk of soil P accumulation and leaching. © 2017, Editorial Department of the Transactions of the Chinese Society of Agricultural Engineering. All right reserved.