This study aimed to investigate the changes in bioactive compounds across the ripening stages of three pepper cultivars, each characterized by unique skin colors. The samples used in this study consisted of three pepper cultivars distinguished by their skin colors as green, purple, and yellow green at breaker ripening stage. Samples were harvested at each of the four ripening stages, including premature, breaker, turning, and mature, and subjected to analysis for various bioactive compounds, including capsaicin, ascorbic acid, kaempferol, quercetin, and sugars. In all cultivars with varying skin colors, the capsaicin content within green pepper fruits consistently increased as the ripening stages advanced. Ascorbic acid was most abundant during the premature stage of development in purple and green cultivars, subsequently declining as maturation progressed. In the case of the purple cultivar, kaempferol content decreased by approximately 30% at the mature stage, while the green cultivar exhibited a gradual increase in kaempferol content with maturation. Conversely, the kaempferol content of the yellow green cultivar rapidly declined as maturation progressed. Regarding quercetin content, the purple and green cultivars tended to decrease with maturity, while the yellow green cultivar displayed an increasing trend. Furthermore, the accumulation patterns of glucose, fructose, and sucrose, the predominant free sugars in green pepper fruit, demonstrated an inclination to increase as the maturation stage advanced in both purple and green cultivars. In contrast, the yellow green cultivar initially showed an elevation in free sugar content during the immature stage, followed by a minor reduction during maturation and a subsequent rise during the mature stage. Each pepper cultivar, distinguished by its unique skin color, exhibits varying levels of bioactive substances at different ripening stages. Therefore, optimal harvesting and utilization should align with periods when the desired substance content is at its peak.