Abstract Currently, global demand for energy has grown and the search for new ecological energy sources is one of the mostly significant issues we face. The digestion of alternative sources of carbon in anoxic environment produces gas of high calorific value, which is a promising source of alternative energy. Thus, this work aimed to evaluate the biogas production of waste originated from a slaughterhouse industry of pigs and poultry, and from the dairy industry, and to characterize the physicochemical properties and microbiological composition of the biogas-producing biomass. Residues were collected and physicochemical and microbiological parameters were evaluated in four different stages of biogas production. At the end of 42 days, approximately 26 L of methane and 12 L of other gases were produced. The high amount of biogas/methane observed was related to the families Porphyromonadaceae, Tissierellaceae, and Methanobacteriaceae. Although less than 6% of the total reads lack classification at any taxonomic level, our analysis showed that about 50% of the sequences did not present a homologue sequence at the genus level in public databases. Knowledge about changes in the microbial composition and their dominance can provide tools for manipulation, isolation, and inoculation of the microorganisms inside the bioreactors to maximize methane production.