A mathematical analysis of the permeate flux decline during microfiltration of fruit juice with hollow fibers under turbulent flow is presented. Impact of complex fluid flow phenomena on mass transfer is analyzed. A comprehensive analytical model for developing concentration boundary layer was formulated from first principles using integral method. Attempts to model the system considering constant boundary layer thickness (film theory) is inaccurate for developing boundary layer. Gel resistance parameter depending on juice characteristics has significant impact on permeate flux. Specific gel layer concentration has insignificant effect on system performance under total recycle mode but important for batch mode. Theoretical results were compared with experiments in clarification of pomegranate juice with poly(ether ether ketone) and polysulfone hollow fiber membranes. The physical parameters of complex mixture were evaluated by optimizing of the flux profiles in total recycle mode of operation and were successfully applied for prediction of batch mode performance. (c) 2014 American Institute of Chemical Engineers AIChE J 60: 4279-4291, 2014