Membranes are located in a membrane module that physically seals and isolates the feed stream from the permeate flux in membrane bioreactors (MBRs). Therefore, module type, structure, and geometrical configuration are critical design considerations affecting membrane performance in MBRs. In this study, impact of membrane module design on treatment and filtration performance of MBRs was investigated. For this purpose, two flat sheet membrane modules with different outlet structures and module geometries, including rectangular- and D-shaped, were tested. In addition to the differences in outlet structure and module geometry, size of circular structures which supported membranes in rectangular- and D-shaped modules differed from each other. Considering the results, permeate quality was not affected from the change in the module design. However, the most remarkable impact of the module design was observed on the transmembrane pressure (TMP) evolution and fouling potential. D-shaped membrane module including smaller circular structures resulted in a decrease in fouling potential and thus, this module could be operated longer time in comparison to rectangular-shaped membrane module without a severe TMP increase. The observed differences in TMP increase and fouling potential lead to the hypothesis that module design is a critical factor affecting filtration performance in MBRs.