The extraction of caffeine from bioresources using more benign and cost-effective processes is of fundamental relevance towards the finding of alternative (bio)pesticides. Classically, the best attempts to extract caffeine from biomass have resulted in low efficiency and in a large consumption of hazardous organic solvents and/or energy requirements. Here, we report an enhanced and selective extraction of caffeine from guaraná (Paullinia cupana, Sapindaceae) seeds using aqueous solutions of ionic liquids. Several ionic liquids composed of imidazolium or pyrrolidinium cations combined with the chloride, acetate and tosylate anions were investigated. Furthermore, the effect of the cation alkyl side chain length and the presence of functionalized groups were also addressed. Additional conditions such as the ionic liquid concentration, the contact time, the solid–liquid ratio and temperature were further optimized by a response surface methodology. Outstanding extraction yields (up to 9 wt% of caffeine per guaraná dry weight) were obtained at a moderate temperature and in a short-time. The recyclability and reusability of the ionic liquids were also confirmed. For the first time it is shown that aqueous solutions of ionic liquids are superior alternatives for the solid–liquid extraction of caffeine from biomass samples and, as a result, the development of an ionic-liquid-based process is straightforwardly envisaged.