Biogas is a renewable energy resource produced during the anaerobic digestion of various organic substrates. A wide community of microorganisms is involved, including methanogens. These Archaea are the biologic key to the process because they accomplish the methane-forming reaction. Despite its crucial role, the microbiome inside the digester is poorly understood. The aim of this work is to develop bioindicators of efficiency for the anaerobic process through the quantification and characterisation of the methanogens and sulphate-reducing bacteria. From a full-scale digester fed with organic wastes, 31 samples were collected. Temperature, pH, acidity, alkalinity and biogas quantity and quality were monitored over time. The methanogens were detected from the samples both in total and as belonging to different taxa units. These evaluations, by real-time quantitative PCR (RT-qPCR) methods, produced valuable results for Methanosarcina, Methanosaeta, Methanocorpusculaceae and sulphate-reducing bacteria. Methanosarcina was the most abundant family, followed by Methanocorpusculaceae and then Methanosaeta. The methanogen taxa are significantly and directly correlated with each other (p < 0.05). Methanosaeta and Methanocorpusculaceae are present in significantly different amounts at different temperatures. While Methanosaeta levels also change when the organic load increases (t test, p < 0.05), Methanosarcina is more tolerant, and its levels are quite constant. Methanosarcina and Methanosaeta are proposed to be bioindicators of the stability of the process (the first) and of susceptibility (the second) to detect early sufferance conditions in the digester. These methods will be useful in the control and optimisation of an eco-friendly waste-to-energy system.