Technical Abstract: Millions of tonnes of feedlot manure and cotton gin waste are generated in the United States each year. Dairy and feedlot operations in New Mexico produce 1.2 million tonnes of manure annually. Traditionally, manure has been used as a soil amendment in agriculture. However, land application of manure is limited in New Mexico due to problems with salinity, potential groundwater contamination, and limited availability of agricultural land. Waste treatment alternatives are sought. A two-phase anaerobic digestion system was used to evaluate the feasibility of producing methane and soil amendment from mixed agricultural wastes. Cotton gin waste and dairy manure were combined and used as feedstock. Under mesophilic conditions, 48% of the combined waste was converted into biogas. The gas yield was 87m3 of methane per tonne of mixed waste. Methane concentration in the biogas averaged 72%. Gas production with mixed waste increased 35% compared to digesting dairy waste alone. Nutrient analyses of the residuals showed that they could be used as soil amendments. Residual solid material from the two-phase anaerobic digester had a considerably higher nitrogen and lower sodium content than aerobically composted manure. Anaerobic digestion lasted from one to three months and required 0.15 m3 of water per 1 m3 of waste. Aerobic composting of similar waste in New Mexico takes eight to nine months and consumes 1.2 m3 of water per 1 m3 of waste.