In biogas structures, concrete faces aggressive media during anaerobic digestion. Biological activities allow the conversion of organic matter into biogas, leading to a medium characterized by a variability of composition in time and space. In order to ensure the sustainability of this expanding industry, solutions for increasing concrete durability are needed. This study aims to analyse the deterioration mechanisms of different binders focusing on the impact of the binder nature on the medium (biochemical composition) during the digestion. Binders with favourable composition to chemically aggressive media were tested: slag cement (CEM III/B), calcium aluminate cement (CAC) and metakaolin-based alkali-activated material (MKAA), and a reference binder: OPC (CEM I). They were exposed to three anaerobic digestion cycles in liquid phase in laboratory bioreactors. The organic acids and ammonium concentrations of the liquid phase were monitored by GC and HPIC. For OPC and slag cement pastes, the chemical and mineralogical changes were characterized by SEM/EDS and XRD. Locally, the presence of binder materials has an impact on the kinetics of the digestion reaction, and therefore on the quantities of gas produced. Ammonium concentrations were above the XA3 class range. Under the conditions explored, biodeterioration mainly led to the carbonation of cement pastes.