Iberis amara L. medicinal herb is well-known for having pharmacological values although its use has been challenged by the low levels of secondary metabolites. To address this issue, this study focused on evaluating the effect of explant, photoperiod, and plant growth regulators (PGRs) to find the optimum medium for inducing callus and establishing cell suspension in I. amara, followed by investigating the chitosan effect on some secondary metabolites. From our observations, the optimum condition for induced callus was achieved from the leaf explants in Murashige and Skoog (MS) media completed with 3 mg L− 1 6-benzylaminopurine(BAP) and 1 mgL− 1 1-naphthalene acetic acid(NAA) under 16-h light/8-h dark photoperiod. The MS enhanced with 3 mgL− 1BAP, 1 mg L− 1NAA, and 2% (w/v) sucrose appeared to be optimum conditions for suspension establishment. Thus, the cells were exposed to different concentrations of chitosan (200, 100, 50, and 0 mg L− 1) in their exponential growth stage from day 8 to 12 and day 12 to 16 following sub-cultures (T1) and sub-cultures (T2), respectively. The results showed that the 50 mgL− 1 chitosan significantly improved the total phenol, flavonoid, flavonol, and anthocyanin content in the I. amara in a dose-dependent manner. The highest malondialdehyde (MDA) amount, as a result of lipid peroxidation, was observed under the 200 ppm chitosan elicitation. Overall, these novel findings demonstrated the possibility of applying the cell suspension of I. amara treated with chitosan as a helpful approach for improving synthesizing phenolic compounds under controlled and sterile conditions without genetic modifications in medicinal herbs.