Concrete structures of anaerobic digestion plants face chemically aggressive conditions due to the contact with the complex liquid fraction of the fermenting biowaste. This paper aims to determine the biogeochemical dynamic interaction phenomena at play between the biowaste and cementitious matrices at the local scale, and to identify durable binders in such environments. Binder materials likely to show increased durability – slag and calcium aluminate cement, and a metakaolin-based alkali-activated geopolymer – and a reference Portland cement were inserted into sealed bioeactors during 5 cycles (245 days) of broken maize anaerobic digestion. Cementitious pastes suffered chemical and mineralogical alteration related mainly to carbonation and leaching. However, they had no negative impact on the bioprocess in terms of pH, metabolic evolution of volatile fatty acids and NH4+, planktonic microbial community composition or CH4 production. In all reactors, the microbial community was able to perform the anaerobic digestion successfully. The MKAA was only slightly altered in its outermost layer. Its presence in the biowaste induced lower NH4+ concentrations, a slightly higher pH and a marked shift in the microbial community, but CH4 total production was not affected. Substantial enrichment of acid forming bacteria, especially members of the genus Clostridium, was observed in the biofilm formed on all materials. Keywords: Anaerobic digestion, cementitious materials, geopolymer, durability, biodeterioration, biofilm