This study investigated the deterioration behavior of the metakaolin based alkali-activated mortar (MK-M), flay-ash-based alkali-activated mortar (FA-M) and granulated blast furnace slag powder-based alkali-activated mortar (SG-M) under simulated microbial induced acid corrosion (MIAC). For comparison, the MIAC induced corrosion of the Ordinary Portland cement-based mortar (OPC) was also studied. The pH variation of the corrosive solution (sulfur oxidizing bacteria liquid medium), visually observation, and mass loss were monitored to estimate the deterioration. X-ray diffraction (XRD), scanning electron microscope (SEM) and thermogravimetric analysis (TGA) were used to analyze the composition and morphology of different samples. The results revealed that the three alkali-activated cement-based mortars displayed a higher alkalinity compared to the Portland cement-based mortar. MK-M and SG-M exhibited better resistance to MIAC with a smooth surface and without the formation of typical corrosives owing to the stable structure of N-A-(S)–H and the lower content of calcium ion. However, SG-M suffered severe corrosion, which was similar to OPC-M, with the formation of abundant gypsum and ettringite and visually changed morphology for its high content of calcium ion and degenerated structure.