With the implementation of municipal solid waste source segregation, the enormous sorted biogenic waste has become an issue that needs to be seriously considered. Anaerobic digestion, which can produce biogas and extract floating oil for biodiesel production, is the most prevalent treatment in China for waste management and greenhouse gas (GHG) emissions reduction, in accordance with Sustainable Development Goal 13 of the United Nations. Herein, a large-scale biogas plant with a capacity of 1000 tonnes of biogenic waste (400 tonnes of restaurant biogenic waste and 600 tonnes of kitchen biogenic waste) per day was investigated onsite using material flow analysis, and the parts of the biogas plant were thoroughly analyzed, especially the pretreatment system for biogenic waste impurity removal and homogenization. The results indicated that the loss of the total biodegradable organic matter was 41.8% (w/w) of daily feedstock and the loss of biogas potential was 18.8% (v/v) of daily feedstock. Life cycle assessment revealed that the 100-year GHG emissions were −61.2 kgCO2-eq per tonne biogenic waste. According to the sensitivity analysis, pretreatment efficiency, including biodegradable organic matter recovery and floating oil extraction, considerably affected carbon reduction potential. However, when the pretreatment efficiency deteriorated, GHG benefits of waste source segregation and the subsequent biogenic waste anaerobic digestion would be reduced.