It was found that both diesel fuel and spent engine oil visibly influenced the number of methanogenic bacteria—a microbial group directly responsible for the biogas production, after 7 days of the process, while after 14 days the effect was not observed. The differences in results between 7th and 14th day of the experiment concerning the numbers of bacteria can be probably explained by microbial adaptation to the process condition. Comparison of the results of numbers of methanogenic bacteria and sulphate reducingbacteria in the presence of diesel fuel (which was probably not sotoxic to microorganisms) can reflect the competitive mechanism for protons—the increase in number of methanogenic bacteria is accompanied by the decrease in sulphate-reducing microorganisms.