Selenium (Se) and iodine (I) are not essential for plant metabolism, however, they are important to humans and animals, and therefore their presence in trace amounts in food is beneficial. Crop fertilization programs provided by Se and I allow for mineral biofortification of the crop and further accumulation of more antioxidants in the plant's edible organs. Therefore, the exogenous application of Se or I may offer a potentially interesting approach to enhancing crop yield and quality. This study aimed at investigating the effect of Se or I application on growth traits, chlorophyll content, fruit yield, and fruit quality (antioxidant capacity) of pepper plants. Growth traits (e.g., shoot length, plant leaf area, plant leaf number, shoot fresh weight, and shoot dry weight), chlorophyll content, plant fruit yield, and fruit quality traits (e.g., vitamin C, capsaicin, and β−carotene contents) were gradually increased with incremental increases in Se and I concentration, applied as a foliar spray (FrS) or through irrigation water (IrW), compared to the control. Maximum values of growth traits, chlorophyll content, and plant fruit yield were obtained with 20 or 40 mg Se L–1 applied as FrS or through IrW, respectively, and with 2.5 or 1.0 mg I L–1 applied as FrS or through IrW, respectively. While maximum values of fruit quality traits were obtained with 40 or 50 mg Se L–1 applied as FrS or through IrW, respectively, and with 7.5 or 5.0 mg I L–1 applied as FrS or through IrW, respectively. However, the Se-IrW treatments were better than the I-FrS treatments. Therefore, this report recommends the utilization of 40–50 mg Se L–1 applied through irrigation water to reinforce pepper plant growth and yield with high quality (antioxidant capacity).