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This paper specifically investigates the effect of an acid producing fungus and anaerobic sulfate reducing bacteria (SRB) on nanophase modified fly ash (FA) concrete specimens. Four different types of concrete specimens namely FA (FA concrete with 40 wt % replacement of Ordinary Portland Cement), FAT (FA concrete modified with 2 wt % TiO2), FAC (FA concrete modified with 2 wt % CaCO3), and FATC (FA concrete modified with 2 wt % TiO2:CaCO3) were fabricated. These specimens were exposed to microbial cultures for accelerated biodeterioration studies. Growth of microbes on specimen surfaces was visualized by epifluorescence microscopic studies. Important biodeterioration parameters like pH reduction, weight loss, thickness, and diameter loss under biofilms were analyzed. Absence of degradation phases like ettringite and calcium oxalate in the modified FA concrete was confirmed using X‐ray diffraction studies. Results proved biodeterioration resistance of all the three nanophase modified FA concrete specimens. Among the three, FAT emerged superior with excellent resistance to biodeterioration owing to the presence of TiO2 nanoparticles. © 2018 American Institute of Chemical Engineers Environ Prog, 38: 457–466, 2019