Biodigesters have been widely used due to their application in wastewater treatment, environmental mitigation, and renewable energy generation. As the consumption of dairy products increases, the wastewater generation increases as well. Therefore, it is necessary to pursue new alternatives to treat dairy industry residues, especially whey effluents. The objective of this work was to test the effects of different substrates and beds on the dynamics of anaerobic degradation and gas production using a bench-scale biodigester. During the experiments, pH variations and gas production were monitored as indicators of microbial activity. The beds that prevented substantial pH falls were most likely to have produced high quality gases, with higher methane content. The substrates that led to highest gas production presented high hydrolysis rates, while the complex substrates allowed for long-term gas production due to slow hydrolysis. Thus, the use of biodigesters can contribute to the mitigation of environmental impacts, encouraging wastewater treatment and supplying a renewable energy source.