Cross-flow microfiltration (CFM) combined with ultra-clean or aseptic packaging offers a promising solution to meet consumer demand for more natural, non-heat treated ready-to-drink fruit beverages. However, membrane fouling can significantly reduce the efficiency of CFM and increase the production cost. To address this issue, we studied the effect of backpulsing on the performance of a semi-industrial CFM equipment featuring 2 m2 of ceramic membranes with 0.2 μm pore size. Using an optimum transmembrane pressure of 150 kPa, we found that backpulsing with a high frequency (every minute) at the beginning of microfiltration and then slowing down the frequency (every 2 min) resulted in higher (+14%) and more consistent average fluxes (100 l.h−1.m−2) while reaching volumetric concentration ratio up to 11. Additionally, the overall specific energy requirements are reduced by 12.5% to 0.0376 kWh.l-1 of treated juice, which is the lowest value among all known de-bacterizing processes, including thermal pasteurization. Importantly, our results showed that backpulsing reduces the retention of the main bioactive compounds of blackberry, including anthocyanins and ellagitannins. These findings demonstrate that CFM with backpulsing is a more cost-effective process that allows for the production of stabilized fruit juices with higher content of bioactive compounds.