Deterioration of concrete in sewer systems is a worldwide pathology leading to premature aging of concrete pipes. Strong deterioration of concrete is mainly due to microorganisms, especially to sulfur-oxidizing bacteria (SOB) which produce sulfuric acid. Mortars made either with ordinary Portland cement (OPC) or calcium aluminate cement (CAC) have been exposed in a waste water collector for five years. Mortar microstructure was observed by microscopy with observations under scanning electron microscopy (SEM) to determine the thickness of the degraded zone. Moreover, the diversity of bacterial communities on biofilms collected at the mortar surface was characterized by using 16S rRNA sequencing. Microstructural approach demonstrated that CAC mortar was less deteriorated than OPC mortar when exposed for five years. Similar bacterial diversities were observed for OPC and CAC samples, but strong differences of relative abundance were evidenced. Both total bacterial and neutrophilic sulfur-oxidizing bacteria (NSOB) populations were smaller for CAC mortar compared to OPC mortar. In the reported in situ conditions, leading to the first stages of biodeterioration only involving NSOB, the better performance of mortar made with CAC is expected to be mainly due to lower abundances of both total bacterial and NSOB population at its surface. The lower abundance of NSOB in the biofilm formed at the mortar’s surface could be linked to the lower acid neutralization capacity of CAC mortar compared to OPC mortar when pH value is higher 4.