Treatment of dairy effluent by membrane filtration permits to recover both reusable water and nutrients, but its advantages are weakened by concentration polarization and subsequent membrane fouling as they cause flux decline and permeate quality deterioration. In order to control flux decline, model dairy effluent was treated by shear-enhanced membrane filtration in this study, and the role of foulants was analyzed. For ultrafiltration (UF) of dairy effluent, protein adsorption and deposition caused flux decline and hydrophilic modification of membranes can reduced this fouling. While for nanofiltration (NF), flux decline was mitigated by the presence of casein micelles, and when the caseins were removed by UF pretreatment, whey proteins would agglomerate through calcium bridges, resulting in severe flux decline during NF concentration. Even if most of proteins were retained by UF pretreatment, free calcium ions increased due to the absence of casein micelles, also inducing flux decline at high concentration factor. Thus, the two-step UF/NF process was not found advantageous as it did not improve the average permeate flux nor permeate quality, while increasing significantly the process energy consumption. This conclusion was valid not only for rotating disk module (RDM) but also for vibratory shear-enhanced process (VSEP), which is available in large membrane area with a low energy consumption.