Polyphenols extracted from blueberry (Vaccinium corymbosum) pomace were concentrated using nanofiltration. Crossflow filtration was shown to be a feasible method for concentrating the polyphenols present in dilute aqueous solutions. High-performance liquid chromatography was employed for the determination of total anthocyanins, total flavonols and chlorogenic acid in the hot water extract. Both nanofiltration membranes (NF245 and NF270) showed complete rejection of phenolic compounds at good permeances, whereas crossflow mode of filtration was found to reduce membrane fouling considerably. Furthermore, a suitable protocol was developed for clean-in-place of the used membranes. After repeated filtrations followed by the cleaning protocol, the rejection performance was preserved unaltered and the relative permeance was recovered up to 73% for NF245 membrane and more than 99% for NF270 membrane.