Membrane fouling is a major obstacle in membrane bioreactors (MBRs) that treat wastewater. The addition of powdered activated carbon (PAC) is commonly suggested as a way to improve the MBR wastewater treatment process with respect to membrane fouling and effluent quality. Integrating the PAC addition into the MBR may also improve the stability of the acclimated microbial community for biodegrading the recalcitrant organic compounds that can also enhance membrane fouling. In this study, the ability of the MBR-PAC system to decrease membrane fouling was evaluated. Two pilot-scale reactors were operated: one reactor was supplemented with suspended PAC, and one was operated under similar conditions, without PAC. The feed to the reactors comprised domestic and olive oil mill wastewater. Surprisingly, the permeate flux and the membrane permeability decreased faster in the MBR supplemented with PAC compared to the control reactor. Corroborating these MBR fouling results, soluble microbial products (SMPs), originating from the PAC-supplemented reactor, were found to be more adhesive to an ultrafiltration membrane mimetic surface (polyether sulfone) as analyzed in a quartz crystal microbalance with dissipation monitoring (QCM-D). While the PAC had almost no effect on the dissolved organic carbon in the MBR, it altered the molecular weight distribution of the organic molecules in the SMP as observed with gel permeation chromatography: The fractions of 577–789 kDa and the one bigger than 4 × 103 kDa, were elevated and reduced, respectively, by the addition of PAC. A biofilm formation analysis using a confocal laser scanning microscopy showed a higher amount of biofilm on the membrane taken from the PAC reactor, but this membrane showed no traces of PAC particles when analyzed with a scanning electron microscope (SEM). Taken together, altering the composition of the dissolved organic matter in the MBR by PAC addition promoted its adhesion to the membrane, induced biofilm formation, and more prominently, decreased membrane permeability.