Digesters produce biogas from organic wastes through anaerobic digestion processes. These digesters, often made of concrete, suffer severe premature deterioration caused mainly by the presence of fermentative microorganisms producing metabolites that are aggressive towards cementitious materials. To clarify the degradation mechanisms in an anaerobic digestion medium, ordinary Portland cement paste specimens were immersed in the liquid fraction of a running, lab-scale digester for 4 weeks. The anaerobic digestion medium was a mixture of a biowaste substrate and sludge from municipal wastewater treatment plant used as a source of anaerobic bacteria. The chemical characteristics of the anaerobic digestion liquid phase were monitored over time using a pH metre, high performance liquid chromatography (HPLC) and ion chromatography (HPIC). An initial critical period of low pH in the bioreactors was observed before the pH stabilized around 8. Acetic, propionic and butyric acids were produced during the digestion with a maximum total organic acid concentration of 50 mmol L− 1. The maximum ammonium content of the liquid phase was 40 mmol L− 1, which was about seven times the upper limit of the highly aggressive chemical environment class (XA3) as defined by the European standard for the specification of concrete design in chemically aggressive environments (EN 206). The changes in the mineralogical, microstructural and chemical characteristics of the cement pastes exposed to the solid and liquid phase of the digesters were analysed at the end of the immersion period by X-ray diffraction (XRD), scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectrometry (EDS) and electron-probe micro-analysis (EPMA). A 700-μm thick altered layer was identified in the cement paste specimens. The main biodeterioration patterns in the bioreactors' solid/liquid phase were calcium leaching and carbonation of the cement matrix.