The selective extraction of capsaicinoids and carotenoids from chili guajillo "puya" flour was studied. When ethanol was used as solvent, 80% of capsaicinoids and 73% of carotenoids were extracted, representing an interesting alternative for the substitution of hexane in industrial processes. Additionally, when the flour was pretreated with enzymes that break the cell wall and then dried, extraction in ethanol increased to 11 and 7% for carotenoid and capsaicinoid, respectively. A selective two-stage extraction process after the treatment with enzymes is proposed. The first step uses 30% (v/v) ethanol and releases up to 60% of the initial capsaicinoids, and the second extraction step with industrial ethanol permits the recovery of 83% of carotenoids present in the flour.