Color and pungency are the two main factors of chili peppers that determine their quality and final market price. In this study, we investigated the effect of light-emitting diodes (LEDs) on fruit color and primary and secondary metabolites (capsaicinoids) in Capsicum annuum L. cv. Cheonyang. High-performance liquid chromatography analysis of acetonitrile extract of chili fruits revealed enhanced capsaicinoid contents in blue LEDs (180 ± 6.32 mg/100 g) when compared with fluorescent light (54 ± 3.12 mg/100 g). However, color of chili pepper was remarkably changed under different light treatments. Among these, high ASTA color values and chromatic parameters (L*, a*, b*, C*, and H°) were recorded under red plus blue LED, further indicating red plus blue LED is responsible for most vivid color development compared with monochromatic red or blue LEDs. In addition, we found total carbohydrate [22.32 mg·g−1 fresh weight (FW)], reducing sugars (8.27 mg·g−1 FW), starch (14.05 mg·g–1 FW), carotenoids (6.15 mg·g−1 FW), and protein (4.83 mg·g−1 FW) were significantly high under red plus blue LED. These results showed that there were significant differences of plant growth and production of various metabolites among the different LEDs. Furthermore, blue LED showed a relatively higher rate of capsaicinoid production and red plus blue LED produced striking color development in chili peppers. Therefore, the results presented here might serve as an alternative strategy for nutritional improvement (color, oleoresin, and pungency) of chili peppers.