The aim of the current study was the exploitation of agro-industrial wastes or by-products such as olive mill wastewater (OMW) and defective wines. A cost-effective system for their maximum exploitation is suggested, using a combined process of membrane filtration and other physicochemical processes. Wastewaters are first treated in a membrane system (prefiltration, ultrafiltration, nanofiltration, and reverse osmosis) where pure water and other organic fractions (by-products) are obtained. Organic fractions, called hereafter byproducts and not wastes, are further treated for the separation of organic compounds and isolation of high added value products. Experiments were performed with OMW and defective wines as characteristic agro-industrial wastewaters. Profit from the exploitation of agro-industrial wastewaters can readily help the depreciation of the indeed high cost process of membrane filtration. The simple phenolic fraction of the OMW was successfully isolated from the rest of the waste, and problems occurring during winemaking, such as high volatile acidity and odours, were tackled.