Centralized biological treatments, i.e., anaerobic digestion (AD) and in-vessel composting (IVC), were supposed to be the promising processes for the disposal of food waste (FW) after source separation, while the systematic benefits were unclear for FW with high water content, salt and oil and thus influenced the selection by the local decision-makers. In this study, two large-scale working AD and IVC plants were compared for environmental impacts, nutrient recovery and economic benefits. For unit amount of FW, 89.26 kg CO2-eq was released in IVC mainly due to 47.89 kWh electricity consumption, and 57.02 kg CO2-eq was produced in AD. With the application of compost and energy recovery, 26.88 and 93.55 kg CO2-eq savings were obtained in IVC and AD, respectively. NH3 emissions were the main contributor to acidification (0.35 kg SO2-eq) in IVC, while AD exerted less impact on acidification (0.09 kg SO2-eq) and nutrient enrichment (0.25 kg NO3-eq) attributed to the counteract of energy recovery. 2029 would be the inflection point for global warming potential in AD with more clean energy applied in electricity mix in China. For nutrient recovery, more C (8.3%), N (37.9%) and P (66.7%) could be recovered in compost, while those were discharged via leachate and biogas residue in AD. The cost of IVC was 16 CNY/t (2.40 USD/t) lower than AD. Combing the three key indexes and the sale routes of products, IVC was recommended to be used in areas dominated by agriculture and forestry industries, and AD was more suitable for large cities. Display omitted •Environmental impacts, nutrient recovery and economic benefits were co-considered.•62.38 kg CO2-eq/t of GWP was produced by IVC mainly for 47.89 kwh electricity input.•36.53 kg CO2-eq/t saving of GWP was observed in AD for 74.5 Nm3 biogas recovered.•More C (8.3%), N (37.9%) and P (66.7%) were recovered from IVC compared to AD.•Monte Carlo analysis was performed to assess the uncertainties of IVC and AD.