Fruit processing facilities are looking for ways to reduce water consumption to counter the impact of climate change. A good alternative is an MBR system to treat the processing wastewater, followed by tertiary treatment using a reverse osmosis (RO) unit to enable water reuse. However, fouling of the RO membrane causes operational challenges. As a result, experiments were completed on treated fruit processing wastewater to identify the causes of fouling that originated from the MBR effluent and develop best management practices (BMPs) to minimize fouling of the RO membrane. Physical and chemical analyses along with visual inspection of the membrane surface using scanning electron microscopy (SEM), energy diffusive X-ray (EDX) and Fourier transform infrared (FTIR) spectroscopy were completed. The issue of RO membrane fouling and subsequent flux decline was directly related to the presence of soluble microbial products, specifically dissolved organic matter (DOM) in the MBR effluent. The developed BMPs show that the previously completed enhanced coagulation-GAC sorption process, when combined with an online non-chemical flushing regimen and proper membrane preservation, keeps the flux readings high, resolving frequent fouling and cleaning problems of the RO membrane.