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Methane and ethanol were co-produced from different feedstock, including a mixture of dairy manure and soybean straw (DMS), a mixture of pig manure and soybean straw (PMS), and soybean straw alone (SS), after anaerobic digestion times of 30 and 60 days in mesophilic conditions. Digesting DMS for 60 days led to the highest methane yield of 115.3 g/kg dry raw feed; however, the lowest ethanol yield of 88 g/kg dry raw feed was observed. After 30 days, SS yielded the lowest methane levels (45.2 g/kg dry raw feed) but the highest ethanol levels (113.5 g/kg dry raw feed). Analysis of the net energy balance showed that the highest net energy balance, 6549 kJ/kg of dry raw feedstock, was achieved from the digestion of DMS for 60 days. Overall, both the type of feedstock and length of digestion time played important roles in the integrated processing of methane and ethanol from livestock manure and straw.