More sustainable waste management in the winery and olive oil industries has become a major challenge. Therefore, waste valorization to obtain value-added products (e.g., polyphenols) is an efficient alternative that contributes to circular approaches and sustainable environmental protection. In this work, an integration scheme was purposed based on sustainable extraction and membrane separation processes, such as nanofiltration (NF) and reverse osmosis (RO), for the recovery of polyphenols from winery and olive mill wastes. Membrane processes were evaluated in a closed-loop system and with a flat-sheet membrane configuration (NF270, NF90, and Duracid as NF membranes, and BW30LE as RO membrane). The separation and concentration efficiency were evaluated in terms of the total polyphenol content (TPC), and by polyphenol families (hydroxybenzoic acids, hydroxycinnamic acids, and flavonoids), using high-performance liquid chromatography. The water trans-membrane flux was dependent on the trans-membrane pressure for the NF and RO processes. NF90 membrane rejected around 91% of TPC for the lees filters extracts while NF270 membrane rejected about 99% of TPC for the olive pomace extracts. Otherwise, RO membranes rejected more than 99.9% of TPC for both types of agri-food wastes. Hence, NF and RO techniques could be used to obtain polyphenol-rich streams, and clean water for reuse purposes.