Little information exists on the fate of antibiotics, hormones and their associated endocrine activity during manure treatment processes. Thus, the aim of this study was to assess the fate of such emerging pollutants and multiple endocrine activities during manure treatment coupling anaerobic digestion and aerobic/anoxic conditions under mesophilic conditions. The thermophilic anaerobic digestion was also studied. The endocrine activities tested include estrogenic (ER), dioxin-like (AhR), peroxisome proliferator receptor gamma (PPAR ), pregnane X (PXR) and androgenic (AR) activities. Our results showed that antibiotics and steroid hormones were recalcitrant to biodegradation under anaerobic conditions in both mesophilic and thermophilic temperatures. In contrast, antibiotic and hormone removal reached between 76 to 95 % when anaerobic digestion was coupled to aerobic/anoxic treatment. In absence of anaerobic predigestion, hormone removal in aerobic/anoxic conditions was about 40 %; it suggests that the anaerobic predigestion could favour the further elimination of hormones in the anaerobic/anoxic process. The estrogenic activity was mainly removed in the aerobic/anoxic (71%) compartment. The dioxin-like activity appeared to be more recalcitrant to degradation. No others endocrine activities were detected.