Chloride and sodium constitute as the major ions in most saline soils, contributing to salt-induced damage in plants. Research on salt tolerance has mostly concentrated on the sodium toxicity; however, chloride toxicity also needs to be considered to understand the physiological, biochemical, and metabolite changes under individual and additive salts. In this study, we investigated the effect of individual Na + and/or Cl − ions (equimolar 100 mM NaCl, Na + and Cl − salts) using in vitro cultures of four soybean genotypes with contrasting salt tolerance. In general, all the treatments significantly induced antioxidant enzymes activities such as catalase, ascorbate peroxidase, glutathione reductase, guaiacol peroxidase, and superoxide dismutase and osmolytes including proline, glycine betaine, and total soluble sugar (TSS). Both individual (Na + , Cl −) and additive (NaCl) stresses induced more pronounced activation of antioxidant enzyme machinery and osmolytes accumulation in the tolerant genotypes (MAUS-47 and Bragg). The sensitive genotypes (Gujosoya-2 and SL-295) showed higher accumulation of Na + and Cl − , while the tolerant genotypes were found to maintain a low Na + /K + and high Ca 2+ level in combination with enhanced antioxidant defense and osmotic adjustment. Gas chromatography-mass spectrometry (GC-MS)-based metabolomic profiling depicted the association of certain metabolites under individualistic and additive salt effects. The genotypespecific metabolic changes indicated probable involvement of azetidine, 2-furanmethanol, 1,4-dioxin, 3-fluorothiophene, decanoic acid and 2-propenoic acid methyl ester in salt-tolerance mechanism of soybean.