In order to promote the development of the biogas industry, solutions are needed to improve concrete structures durability in this environment. This multiphysics study aims to analyse the multiphases interactions between the liquid phase of an anaerobic digestion system and cementitious matrices, focusing on (i) the impacts of the binder nature on the anaerobic digestion process at local scale, and (ii) the deterioration mechanisms of the materials. Cementitious pastes made of slag cement (CEM III), innovative metakaolin-based alkali-activated material (MKAA), with compositions presumed to resist chemically aggressive media, and a reference binder, ordinary Portland cement (CEM I), were tested by immersion in inoculated cattle manure in bioreactors for a long period of five digestion cycles. For the first time it was shown that the digestion process was disturbed in the short term by the presence of the materials that increased the pH of the liquid phase and slowed the acids consumption, with much more impact of the MKAA. However, the final total production of biogas was similar in all bioreactors. Material analyses showed that, in this moderately aggressive medium, the biodeterioration of the CEM I and CEM III pastes mainly led to cement matrix leaching (decalcification) and carbonation. MKAA showed a good behaviour with very low degraded depths. In addition, the material was found to have interesting ammonium adsorption properties in the chemical conditions (notably the pH range) of anaerobic digestion.