Abstract The paper presents a synthesis of novel hydrophobic deep eutectic solvents (DESs) composed of natural components, which were used for removal of furfural (FF) and 5-hydroxymethylfurfural (HMF) from lignocellulosic hydrolysates. The main physicochemical properties of DESs were determined, followed by explanation of the DES formation mechanism, using 1H NMR, 13C NMR and FT-IR analysis and density functional theory (DFT). The most important extraction parameters were optimized. Reusability, regeneration of DES, multistage extraction, influence of FF and HMF concentration, as well as possibility of sugars loss were also investigated. The experimental studies revealed high extraction efficiency resulting in 79.2% and 87.9% removal of FF and HMF respectively from model hydrolysates and in the range of 74.2–76.1% and 87.8–82.3% from real samples in one-step extraction. The yield of bio‑hydrogen production via dark fermentation after the DES extraction was comparable to the results obtained using enzymatic hydrolysis. The theoretical studies on the extraction mechanism revealed that hydrogen bonds and van der Waals interactions were the main driving force for detoxification of lignocellulosic biomass.