The agri-food industry is responsible for generating high volumes of byproducts, representing a largely available and low-cost source of value-added compounds, including, notably, polyphenolic compounds. Among these, lignin has gained increasing attention as a functional additive in a variety of sectors due to its remarkable antioxidant properties. Despite the promising potential of this complex and heterogeneous polyphenol polymer, its exploitation has remained underexplored, mostly due to difficulties related to its recovery from natural sources, primarily woody materials. Recently, common lignin extraction methods, relying on the use of conventional solvents, have been replaced by efficient, sustainable, and cost-effective deep eutectic solvents (DESs). These solvents are easily prepared by mixing a hydrogen bond acceptor and a hydrogen bond donor to form a new solvent with a melting point lower than those of the individual components. The ability to form hydrogen bonds or to donate/accept protons confers DESs good dissolution properties toward phenolic compounds. In this context, we report herein the application of DESs for the efficient extraction of lignin from natural sources, very rich in this polyphenol polymer. For instance, a combination of ball milling and DES-based treatment proved an effective strategy for lignin recovery from edible nut shells. Following ball milling treatment, shells were treated with 1:2 mol/mol chlorine chloride/lactic acid (ChCl/LA2) as DESs at 120 °C for 24 h, yielding lignin at 19- 27% w/w. The extracted lignin exhibited antioxidant properties, particularly in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay (EC₅₀ values ranging from 0.03 to 0.19 mg/mL). In addition, a full valorization of spent coffee grounds and tomato seeds as source of antioxidant compounds was implemented by developing a DES-based (ChCl/LA2) extraction protocol, allowing for the sequential recovery of low-molecular-weight phenols and lignin. The examples that will be presented showcase the potential of lignin as natural antioxidant compound for different applications.