Exploration of two major commercialized flat-sheet and hollow-fiber membranes in a submerged membrane fungi reactor fed with a synthetic textile wastewater revealed striking differences in the extent and mechanism of fouling between the two types, indicating a case-specific scope of choice between the two for industrial wastewater treatment. The hollow-fiber membrane exhibited fouling with a cake layer composed of fungi and starch, intensity being proportional to the operating flux (0.05–0.3 m/d). Conversely, the flat-sheet membrane suffered from immediate internal pore blocking beyond a critical flux of 0.2 m/d. During the experiment with major constituents of the synthetic wastewater separately, while media containing only starch and only dye induced negligible fouling, flux-dependent pore blocking was evident for both the hollow-fiber (0.288 m/d) and flat-sheet membranes (1.3 m/d) for the mixture of starch and dye. Despite a remarkable 99% color and 97% TOC removal achieved by both membranes, fouling with different modes and intensity for the two types under similar conditions and for the same type of membrane under different exposure conditions warrants development of suitable modules for such recalcitrant wastewater.