Anaerobic digestion is a demanding process, due to the large number of process and environmental factors that affect it. Many years of research of the various parameters have made it possible to optimise the process to obtain the maximum amount of biogas and methane contained in it, and this provides energy and environmental benefits. The article deals extensively with the operation of agricultural biogas plants, using the example of a plant that faces numerous operational problems. In order to identify the negative effects on energy yield and the equipment operating in the system, the substrate was examined, the data on its operation analysed, and solutions were proposed that should be taken into account in the further operation of the biogas plant. The analysis showed a good biogas yield from beet pulp of 563 dm3∙kg−1 of TS (total solid) and an average methane yield of 58%. With the analysis presented, it was possible to identify some operational problems. The biogas yield study also highlighted some errors made at the plant design stage. The most important of these is the use of an inappropriate organic matter loading factor for the digester, which leads to acidification of the contents and degradation of the methanogenic microorganism cultures.