Biodeterioration of cementitious materials in sewer networks is a major concern for health and economic reasons. Essentially, it is due to the biological oxidation of H2S into H2SO4 leading to a local progressive dissolution of the cementitious matrix and the precipitation of expansive products likely to provoke cracks. However, it is widely known that CAC has a better performance in such environments but the mechanisms are not very well understood. Nevertheless, previous studies focused mainly on measuring the mass loss of the specimens accompanied with little information on the chemical alteration of the cementitious matrix. This study aims to compare the performance of CAC and BFSC mortars in sewer conditions using laboratory test (BAC-test). Leaching kinetics were evaluated by concentrations measurements of cementitious cations in the leached solutions and of sulphate production by the microorganisms. Moreover, SEM observations coupled with EDS analyses allowed the identification of the chemical alteration of the cementitious matrix.