Design and construction of full-scale anaerobic digesters that co-digest manure with various materials requires analysis of each substrate. Substrate combinations should be analyzed through a scale up procedure in which substrates are characterized, and then evaluated using biochemical methane potential assays (BMPs) and anaerobic toxicity assays (ATAs). The BMPs provide a preliminary indication of the biodegradability of a substrate and of its potential to produce methane via anaerobic digestion, while ATAs determine the degree to which a particular substrate inhibits methane production. Mixture combinations that perform well in BMPs and ATAs should be tested in laboratory-scale anaerobic digesters. Once proven in lab-scale reactors for at least three hydraulic retention times, the best mixture should be tested in a pilot-scale reactor. This paper focuses on the first steps in this process using BMPs and ATAs results to select mixtures for laboratory-scale digester testing. The baseline feedstock was beef manure obtained from concrete feedlot pens (open and covered) in eastern Iowa. Various bedding materials were available, including oat hulls, corn stover, and wood shavings. To provide additional energy production, industrial byproducts from cardboard manufacturing, enzyme production, and corn and soybean processing were also potential substrates. Substrates were characterized for TS, VS, COD, pH, alkalinity, and ammonia. Then BMPs were completed on all substrates and ATAs were performed as needed. The results reported here were used to develop mixtures for use in laboratory-scale anaerobic digester testing.