The industrial-scale production of pigments traditionally relies on chemical synthesis or linear extraction methods using petroleum derivatives, such as volatile organic solvents. Color is a critical sensory attribute that influences consumers’ purchasing decisions and is directly related to the perception of sweetness and food quality. Consequently, there is an unprecedented demand for natural substitutes to meet market preferences for natural and clean-label products. This protocol meticulously describes an alternative process using ionic liquids for the high-performance extraction of carotenoids from food matrices. The methodology includes a detailed statistical experimental design (screening tests, fractional factorial design, and central composite design), evaluating up to six independent variables and their simultaneous effects on carotenoid yield. Additionally, it outlines two procedures for the recovery and reuse of ionic liquids and ethanol used in the extraction process, aiming to enhance ecological sustainability and reduce costs. Finally, the protocol details the method for carotenoid identification using HPLC-MS.