Anaerobic digestion is a biological process that transforms high-strength organic effluents into biogas with multiple benefits. However, concurrent with organics’ biological transformation, a liquid phase with a high solid content is also derived from this process. Valorizing this fraction is not an easy task if an agronomic application cannot be considered as a suitable option. The thermal valorization of this fraction allows for energy extraction but also gives rise to additional capital investment and increases the energy demand of the global process. In addition, the thermal treatment of digestate has to deal with a mineralized material. The changes in organic matter due to anaerobic digestion were studied in the present manuscript, by evaluating the thermal behavior of samples, activation energy, and organic transformation using Fourier transform infrared (FTIR) spectroscopy. Digested samples of a mixture composed of manure and glycerin (5% v/v) were studied. The stabilization caused a dramatic decrease in aliphatic compounds, greatly increasing the mineral content of the sample. Results from differential scanning calorimetry (DSC) indicated an energy content of 11 kJ/g for the feed material and a reduction to 9.6 kJ/g for the long-term stabilized sample. The activation energy of the feed was 249.5 kJ/mol, whereas this value was reduced to 70–80 kJ/mol for digested samples. If the valorization route selected for digestates is thermal conversion, the lower energy content and more complex structure of these materials (higher content of lignin and protein-type compounds) must be carefully evaluated.