The removal efficiency of nine pharmaceutical compounds from primary sludge was evaluated in two different operating conditions: (i) in conventional Mesophilic Anaerobic Digestion (MAD) alone and (ii) in a co-treatment process combining Mesophilic Anaerobic Digestion and a Thermophilic Aerobic Reactor (MAD-TAR). The pilot scale reactors were fed with primary sludge obtained after decantation of urban wastewater. Concerning the biodegradation of organic matter, thermophilic aeration increased solubilization and hydrolysis yields of digestion, resulting in a further 26% supplementary removal of chemical oxygen demand (COD) in MAD-TAR process compared to the conventional mesophilic anaerobic digestion. The highest removal rate of target micropollutants were observed for caffeine (CAF) and sulfamethoxazole (SMX) (>89%) with no substantial differences between both processes. Furthermore, MAD-TAR process showed a significant increase of removal efficiency for oxazepam (OXA) (73%), propranolol (PRO) (61%) and ofloxacine (OFL) (41%) and a slight increase for diclofenac (DIC) (4%) and 2 hydroxy-ibuprofen (2OH-IBP) (5%). However, ibuprofen (IBP) and carbamazepine (CBZ) were not degraded during both processes. Anaerobic digestion affected the liquid-solid partition of most target compounds. Sorbed fraction of pharmaceutical compounds on the sludge tend to decrease after digestion, this tendency being more pronounced in the case of the MAD-TAR process due to much lower concentration of solids. Display omitted •A hybrid digester was implemented to evaluate pharmaceutical compounds removal.•MAD-TAR allowed a better removal of VSS (76%) compared to MAD (47%).•Removal higher than 90% was found for CAF and SMX whatever the process.•Moderate (DIC, 2OH-IBP) to high (OXA, PRO, OFL) removal was observed in MAD-TAR.•Biodegradable compounds removal was correlated with their fraction in liquid phase.