Research was carried out with the aim of monitoring anaerobic digestion processes using thermal analysis with the aid of mass spectrometry so as to define the stability of the digestate obtained. Three different systems were investigated under varying conditions. The digestion of waste sludge from a pharmaceutical industry (PI) and the digestion of cattle manure (CM) were evaluated under mesophilic conditions. The co-digestion of a mixture of primary sludge (PS) and the organic fraction of municipal solid wastes (OFMSW) was studied under thermophilic conditions. Temperature-programmed combustion tests were carried out to investigate the degree of stabilization of samples throughout the digestion processes. The derivative thermogravimetry (DTG) profiles obtained for the mesophilic digestion of PI waste showed a decrease at low temperatures and an increase at high temperatures in the intensity of the peaks recorded as the stabilization process proceeded. These results are in accordance with those obtained by the present authors in their previous work on the mesophilic digestion of primary sludge and OFMSW. In contrast, the DTG profiles obtained from the stabilization process of CM and thermophilic codigestion of PS and OFMSW showed a reduction in peaks at high temperatures. When the stabilization products obtained from CM by anaerobic digestion and by composting processes were compared, it was observed that the composting process was capable of further decomposing materials readily oxidized at low temperatures and increasing the presence of structurally more complex substances. The evolution of the differential thermal analysis (DTA) signal recorded simultaneously showed considerable similarity to the mass/charge (m/z) signal 44 registered by the mass spectrometer. The use of mass spectrometry helped to clarify the inner workings of the digestion process.