This study aimed to determine the effects of 24-epibrasinolide (EBL) and methyl jasmonate (MJ) treatments on growth parameters and secondary metabolite synthesis in adventitious root and cell suspension cultures of Hyoscyamus niger. Therefore, different concentrations (0.5, 1 and 2 mg L−1) of EBL alone and combined with 224.3 mg L−1 (1 mM) MJ were applied to root and cell suspension cultures. 2 mg L−1 and 1 mg L−1 EBL were determined as the treatments in which the highest values were obtained in terms of growth criteria in root and cell cultures, respectively. In root cultures, the highest scopolamine accumulation (2.57 mg g−1) was obtained from the combination of 2 mg L−1 EBL and MJ, while the highest value (0.66 mg g−1) for hyoscyamine was observed in the roots treated with 1 mg L−1 EBL and MJ. In cell cultures, 2 mg L−1 EBL for scopolamine and 0.5 mg L−1 EBL for hyoscyamine were found to be the best applications and calculated as 0.51 µg g−1 and 0.28 µg g−1, respectively. EBL and MJ treatments also stimulated total phenolic content (TPC). The highest TPC in root cultures was detected as 18.01 mg g−1 with the combination of MJ while in cell cultures, maximum TPC was observed in cells applied with 2 mg L−1 EBL and MJ as 11.56 mg g−1. When EBL and MJ were applied to root and cell suspension cultures, significant changes occurred in the amount of phenolic compounds. Co-application of EBL and MJ significantly increased the amount of gallic acid, catechin, epicatechin, cinnamic acid and chlorogenic acid in root cultures. The application of 2 mg L−1 EBL was determined as the most suitable application for gallic acid, catechin, epicatechin, p-coumaric acid, and caffeic acid in cell cultures. It was also found that the metabolite production performance of adventitious roots was higher than that of cells. In conclusion, it was suggested that the use of MJ and EBL may be a promising strategy to enhance the accumulation of scopolamine, hyoscyamine and phenolics in root and cell cultures of H. niger.