Herein, we report on the development of a waste minimization/valorization methodology applied to the representative benchmark Sonogashira cross-coupling reaction performed in a continuous-flow reactor, featuring a continuous-flow downstream membrane organic/aqueous separator to recover medium and products with minimal waste. The protocol is based on the use of a biomass waste-derived heterogeneous Pd-based catalyst, which is obtained from the valorization of urban-waste pine needles (PiNe). In a circular economy approach, the PiNe biomass has been proven to be capable of producing an effective active carbon support for Pd nanoparticle immobilization. In addition, the catalyst has been utilized in an azeotropic mixture formed by industrial wastederived cyclopentyl methyl ether (CPME) and water. Thanks to this combination and with the adoption of flow conditions, high yields of final target products could be accessed with high stability and durability of the catalyst. Final isolation of the products has been realized by setting an in-line liquid−liquid separator in flow, which has also allowed CPME recovery with a significant reduction of the waste generated. The protocol has been applied to the representative preparation of eniluracil, a GSK API.