Spinach and orange by-products are well recognized for their health benefits due to the presence of natural polyphenols with antioxidant activity. Therefore, the demand to produce functional products containing polyphenols recovered from vegetables and fruits has increased in the last decade. This work aims to use the integrated membrane process for the recovery of polyphenols from spinach and orange wastes, implemented on a laboratory scale. The clarification (microfiltration and ultrafiltration, i.e., MF and UF), pre-concentration (nanofiltration, NF), and concentration (reverse osmosis, RO) of the spinach and orange extracts were performed using membrane technology. Membrane experiments were carried out by collecting 1 mL of the permeate stream after increasing the flow rate in 1 mL/min steps. The separation and concentration factors were determined by HPLC-DAD in terms of total polyphenol content and by polyphenol families: hydroxybenzoic acids, hydroxycinnamic acids, and flavonoids. The results show that the transmembrane flux depended on the feed flow rate for MF, UF, NF, and RO techniques. For the spinach and orange matrices, MF (0.22 µm) could be used to remove suspended solids; UF membranes (30 kDa) for clarification; NF membranes (TFCS) to pre-concentrate; and RO membranes (XLE for spinach and BW30 for orange) to concentrate. A treatment sequence is proposed for the two extracts using a selective membrane train (UF, NF, and RO) to obtain polyphenol-rich streams for food, pharmaceutical, and cosmetic applications, and also to recover clean water streams.