Brewer’s spent grains (BSG) offer valuable opportunities for valorization beyond its conventional use as animal feed. Among its components, lignin—a natural polymer with inherent antioxidant properties—holds significant industrial potential. This work investigates the use of microwave-assisted extraction combined with acidic natural deep eutectic solvents (NaDESs) for efficient lignin recovery, evaluating three different NaDES formulations. The results indicate that choline chloride–lactic acid (ChCl-LA), a NaDES with superior thermal stability as confirmed via thermogravimetric analysis (TGA), is an ideal solvent for lignin extraction at 150 °C and 15 min, achieving a balance of high yield and quality. ChCl-LA also demonstrated good solubility and cell disruption capabilities, while microwaves significantly reduced processing time and severity. Under optimal conditions, i.e., 150 °C, 15 min, in the presence of ChCl-LA NaDES, the extracted lignin achieved a purity of up to 79% and demonstrated an IC50 (inhibitory concentration 50%) of approximately 0.022 mg/L, indicating a relatively strong antioxidant activity. Fourier transform infrared (FTIR) and 2D-HSQC NMR (heteronuclear single quantum coherence nuclear magnetic resonance) spectroscopy confirmed the successful isolation and preservation of its structural integrity. This study highlights the potential of BSG as a valuable lignocellulosic resource and underscores the effectiveness of acidic NaDESs combined with microwave extraction for lignin recovery.