The purpose of this work was to investigate the effect of the ripening stage and type of soil on the concentration of carotenoids and vitamins in Habanero pepper (Capsicum chinense Jacq.). Pepper plants were grown in two soils named according to the Mayan classification as: K’ankab lu’um (red soil) and Box lu’um (black soil). The results of two harvests at 320 and 334 PTD (post-transplant day) showed that the ripening stage exhibited a significant effect (p < 0.05) on the concentration of carotenoids and vitamins, while the effect of the soil type was negligible. The concentration of carotenoids decreases as the ripening process of the fruit takes place, with the highest concentration of lutein (49.47 ± 0.34 mg/100 g of dry mass), β-carotene (99.92 ± 0.69 mg/100 g of dry mass) and β-cryptoxanthin (20.93 ± 0.04 mg/100 g of dry mass) in the unripe peppers. The concentration of vitamins increases as the ripening process develops, with the highest concentration of Vitamin E (9.69 ± 0.02 mg/100 g of dry mass) and Vitamin C (119.44 ± 4.72 mg/100 g of dry mass) in the ripe peppers. This knowledge could be used to select the best ripening stage to harvest Habanero peppers according to the use of the pepper and to the needs of producers/company.