Capsicum annuum contains potential therapeutic capsaicinoids, and various stress factors influence plant productivity. Serotonin is an indoleamine involved in signaling several stress response mechanisms in plants. However, the influence of serotonin on cell growth and the accumulation of secondary metabolites, mainly capsaicinoids production, is not yet clearly defined under salt stress. In this study, we optimized chili cell suspension cultures to maximize biomass, capsaicinoids, and phenolic compounds production using response surface methodology with two variables (serotonin and NaCl) of different concentrations in culture media supplemented with 2,4-dichlorophenoxyacetic acid and Kinetin. The results revealed a significant increase in biomass (14.3 g/L FW), capsaicin (0.93 μg/g FW), and dihydrocapsaicin content (0.32 μg/g FW) in chili cell suspension cultures compared with the control. Among all the phenolic compounds, chlorogenic acid was enhanced (17.4 μg/g FW), compared to control cultures. Serotonin exhibited stress mitigation effects and boosted antioxidant potential in chili suspension cultures. The present results illustrated that the optimized conditions can be used in scale-up studies of capsaicinoids production through the bioreactor.