An efficient and eco-friendly extracting process of wood by-products (maritime pine knots and stumps and aspen knots and barks) using a twin-screw extruder has been developed. This continuous device allowed a thermo-mechanical treatment of the woody material to recover fractions containing hydrophilic polyphenols and antiradical compounds. The breakdown of woody materials and the high level of pressing of the solid/liquid mix were mainly influenced by the solvent-to-solid ratio for maritime pine knots and stumps and aspen knots, and by the solvent-to-solid ratio and the barrel temperature in the case of aspen barks. Compared to the extractives content of each by-product determined at laboratory scale, twin-screw extractions were promising for the valorisation of wood by-products and the recovery of bioactive substances.