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This contribution presents an extensive performance evaluation of metakaolin-based geopolymer and calcium aluminate mortars during a long-term field exposure to a wastewater system exhibiting intensive microbially induced acid corrosion (MIAC) conditions. Results were compared to a high-performance OPC concrete, typically used for manhole fabrication. Field conditions were obtained by monitoring relative humidity, temperature, H2S and CO2. Microstructural degradation and elemental distributions within each binder type over time were recorded by electron probe microanalysis, X-ray diffraction and pH-imaging techniques, together with specimen's mass and surface-pH characterization. Microbiome and epifluorescence analyses indicated exposure-time dependent alternating bacterial community structures within the materials. Clear differences regarding bacterial species distribution and biodiversity were observed for the different binder types. Estimated corrosion rates were the lowest (1.4 mm/a) and the highest (13.3 mm/a) for the tested geopolymer formulations, pointing out that only well designed geopolymer materials may provide an improved MIAC resistance.