Allium jesdianum is considered as the most important genera of the Liliaceae family with various pharmacological properties. The present study was carried out to determine the best pre-germination treatment in A. jesdianum. The highest seed germination (58.33%) was observed at chemical treatment including the combination of α-naphthaleneacetic acid (1 mgL− 1) and benzyl aminopurine (3 mgL− 1) on Murashige and Skoog (MS) media. The highest callus induction (86.7%) was observed at MS/2 media, which was supplemented by NAA (1 mgL− 1) and BAP (3 mgL− 1) from hypocotyl explants. Two elicitors including methyl jasmonate (MeJ) (0, 25, 50, and 100 µM) and putrescine (Pu) (0, 0.5, and 1 mM) were used to investigate their effects on lipid peroxidation, callus growth traits, total phenolics content (TPC), the contents of total flavonoids (TFD), total flavonols (TFL), anthocyanin, total chlorophyll, total carotenoids and on antioxidant activity through DPPH (1,1-diphenyl-2-picrylhydrazyl) method under callus culture. The results showed the superiority of MeJ over Pu for increasing the secondary metabolites and antioxidant activity in callused of A. Jesdianum, compared to the control. The highest TPC (6.02 mg GAEg− 1 FW), TFD (0.52 mg QEg− 1 FW), and TFL (0.39 mg QEg− 1 FW) were observed under 50 µM of MeJ. Meanwhile, the highest value for anthocyanin (8.99 µ mol g− 1 FW) was achieved at 25 µM of MeJ. The highest DPPH activities were observed at 50 and 100 µM of MeJ. Putrescine (0.5 mM) elicitation showed only superiority for callus growth rate (0.53 mm day− 1) and carotenoids (0.045 mg g− 1 DW). In this study, effective seed germination and elicitation of A. Jesdianum callus cultures were developed for the first time. Thus, new protocols could be suitable for future studies in biotechnological aspects of this medicinal plant.