The effects of magnetic field (MF) treatments of soybean seeds on calli growth, cell damage, and biochemical changes under salt stress were investigated under controlled conditions. Soybean seeds were exposed to a 1.0 Hz sinusoidal uniform pulsed magnetic field (PMF) of 1.5 µT for 5 h/day for 20 days. Non-treated seeds were considered as controls. For callus regeneration, the embryonic axis explants were taken from seeds and inoculated in a saline medium with a concentration of 10 mM NaCl for calli growth analysis and biochemical changes. The combined treatment of MF and salt stress was found to significantly increase calli fresh weight, total soluble sugar, total protein, and total phenol contents, but it decreased the ascorbic acid, lipid peroxidation, and catalase activity of calli from magnetically exposed seeds compared to the control calli. PMF treatment significantly improved calli tolerance to salt stress in terms of an increase in flavonoid, flavone, flavonole, alkaloid, saponin, total polyphenol, genistein, and daidzein contents under salt stress. The results suggest that PMF treatment of soybean seeds has the potential to counteract the adverse effects of salt stress on calli growth by improving primary and secondary metabolites under salt stress conditions.