BACKGROUND A wide variety of secondary metabolites are synthesized from primary metabolites by plants which have a vast range in pharmaceutical, food additive and industrial applications. In recent years, the use of elicitors has opened a novel approach for the production of secondary metabolite compounds. Dracocephalum kotschyi is a valuable herb due to pharmaceutical compounds like rosmarinic acid, quercetin and apigenin. In the current study, foliar application of chitosan (0, 100, 400 mg L−1) as an elicitor was used. RESULTS After chitosan treatment, the amounts of hydrogen peroxide (H2O2) increased and the plant was able to increase the activities of enzymatic (guaiacol peroxidase, catalase and phenylalanine ammonium lyase) and non‐enzymatic (total phenols and flavonoids) defensive metabolites. Also, foliar spray of chitosan promoted nutrient absorption which led to the accumulation of macroelements in the plant. CONCLUSIONS Chitosan was found to be a very effective elicitor for improving rosmarinic acid and quercetin content (up to 13‐fold). Also, the content of apigenin (anticancer flavonoid) showed 16‐fold enhancement compared to the control. Therefore, the treatment of D. kotschyi leaves with chitosan caused a very large increase in the induction and production of important pharmaceutical compounds such as rosmarinic acid and quercetin. © 2020 Society of Chemical Industry