Anaerobic digestion has been demonstrated to be an attractive process for the treatment of manure, municipal sewage sludge and industrial wastes. The residues from the digestion, called digestates, are commonly used as soil improvers or organic fertilizers. In Nitrate Vulnerable Zones (NVZs), thermal drying is a promising post-processing. Concentrating the nutrients (nitrogen and phosphorus) reduces the cost of transport towards areas that require soil conditioner and/or fertilizer. Hygienisation of the final product can also be expected, depending on the temperature-time drying conditions (Carrington, 2001; Romdhana et al., 2009). Digestates may contain a range of zoonotic pathogens including, bacteria, viruses, parasites (Cunault et al., 2011). The proposed work aimed at characterizing the influence of the drying conditions on the survival of selected indicator microorganisms. Drying experiments were conducted in a closed loop drying system, using moist air as drying medium in a through-flow chamber. The air temperature was investigated in the range of 70 to 140°C. Digestates were sampled in an agricultural plant and in two plants treating mainly the organic fraction of municipal solid wastes. Two types of bacterial indicators were selected to cover a range of thermoresistance: Escherichia coli, a bacteria most sensitive to thermal inactivation, and sulfite-reducing anaerobes (SRA), a group of the most resistant and sporulating bacteria. As Clostridium perfringens is commonly used as an indicator of treatment efficiency, its proportion in SRA was also quantified. As expected, the results showed that the ability of drying for inactivating the pathogens depends both on the target pathogen and on the temperature-time conditions. Contrary to E. Coli, C. perfringens is unaffected by a treatment at 70°C for 1 hour. Thermotolerance can be represented by the decimation time, DT. For each pathogen, the values of DT were deduced from the experiments.