The durability of cementitious materials in harsh environments, like marine or sulfate-rich soils, is influenced by various factors, with bacteria playing a significant role alongside environmental chemistry. To address sustainability concerns, research focuses on developing cement mixes that reduce emissions and withstand aggressive conditions. New standards require testing these mixes. This study developed and tested low-carbon cement mixes (CEM III, CEM V, CAC, and CSS) under real sewer conditions enriched with H2S and bacteria for four years. The specimens underwent SEM-EDS, XRD, TGA-DTA, and µRaman analysis to enhance understanding of degradation processes by conducting detailed and localized characterization of both initial and newly formed phases. Through this analysis, the work offers a precise description of the effects of bio-alteration on various cement matrices, elucidating their reactions under such conditions. The analysis of mortar specimens has revealed the presence of expansive products such as gypsum besides various polymorphs of calcium carbonate.