This study aims to evaluate the performance of low calcium fly ash based geopolymer (FA-GPm) and alkali-activated slag based mortars (AASm) in comparison to sulphate resistant Portland cement mortar (SRm) in an aggressive sewer environment. pecimens were extracted from field exposure after 24 months. Visual, chemical and physical analyses were performed to evaluate the corrosion and degradation. Surface pH was evaluated to identify the microbial induced corrosion (MIC) stage in each specimen. Compressive strength of these mortar cubes was also evaluated after 2 years of exposure to measure the deterioration of strength. The neutralization depth of the specimens was measured by using the phenolphthalein indicator to observe the penetration of H2S and CO2. Extensive microstructural analyses were carried out to assess the extent and type of deterioration of gel matrix by using techniques such as scanning electron microscopy (SEM), energy dispersive X-Ray (EDX) and X-Ray diffraction (XRD). Results showed greater depth of neutralization and surface pH reduction in FA-GPm as compared to AASm. Further investigation on penetration of sulphur confirmed much higher diffusion in FA-GPm as compared to AASm. XRD and SEM with EDX analysis showed the crystallization of thernadite and gypsum within the matrix of FA-GPm and AAS mortar, respectively. Extend of overall matrix deterioration was much higher in FA-GPm as a result of thernadite crystallization as compared to AASm after 24 months of exposure.