The aim of this study was to determine the effect of electromagnetic microwave radiation on the activity of microorganisms during the anaerobic digestion of dairy wastewater. The substrate used in the study was a model dairy wastewater prepared with the use of milk powder. The anaerobic sludge was taken from the anaerobic reactor operated at mesophilic conditions, then it was heated by microwave irradiation (Option 1) or heated in a conventional thermostatic cabinet (Option 2). The study, based on the temperature of the process, was divided into two stages. In the first stage, the temperature of the process was 38°C and in the second stage it was 58°C. The studies showed that the use of microwave electromagnetic field might influence on the biogas production. Furthermore, microwave treatment of anaerobic sludge enhanced the removal of organic compounds in the methane fermentation process.