Many pepper cultivars can be raised under artificial lighting in a plant factory. An easily measured parameter is needed to fast predict fruit loading in pepper cultivars. In this study, four pepper cultivars with contrasting manners in growth and fruiting were cultured under three light-emitting diode (LED) spectra in comparison with a sunlight control. It was found that the red-light spectrum (71.7% red-, 13.7% green-, 14.6% blue-lights) increased over 40% of dry mass in fruits, while the green-light spectrum (26.2% red-, 56.4% green-, 17.4% blue-lights) induced no fruiting compared to the control. Only two cultivars responded by fine root morphology, which was characterized as smaller surface-area and fewer tip-number in the blue-light spectrum (7.8% red-, 33.7% green-, 48.5% blue-lights) than in red LED light. Tip-number showed a negative correlation with fruit dry-mass in three cultivars, while fine root diameter increased with dry mass in fruits. In conclusion, fine root tip-number can be used as a predictor of fruit dry-mass in pepper cultivars high in fruit quality or yield. The red-colour light was recommended for raising pepper cultivars in a plant factory with the purpose of greater fruit productivity.