The current study aimed to evaluate and compare the effect of different concentrations (0.0–200.0 µM) of jasmonic acid (JA), methyl jasmonate (MeJA), and salicylic acid (SA) on suspension culture mass production and untargeted metabolic profiling of the medicinal plant Cymbopogon schoenanthus subsp. proximus. The addition of 50 µM MeJA improved the fresh weight of embryogenic tissue significantly. MeJA and SA did not affect tissue dry weight, whereas JA significantly decreased it. Based on 1H and 1H–13C NMR data and NMR databases, 50 compounds were identified. The addition of stress hormones resulted in the biosynthesis of novel metabolites like theophylline and syringate that were absent in control samples. In addition, significant variations in the concentrations of numerous compounds, including sugars, amino acids, organic acids, phenols, and alkaloids, were observed. The upregulation of trigonelline concentration was observed upon the addition of a higher concentration of MeJA (200 µM), whereas all tested concentrations of SA resulted in its upregulation. Addition of JA and SA causes significant changes in aminoacyl-tRNA biosynthesis pathway and amino acid metabolism pathways, such as alanine-aspartate and glutamate metabolism and arginine and proline metabolism. MeJA had significant impacts on glycolysis and starch-glucose metabolism pathways in addition to amino acids metabolism pathways. The present findings were successful in demonstrating a correlation and distinction between the effects of JA, MeJA, and SA, on the metabolome of Cymbopogon schoenanthus, a valuable medicinal plant. The identified metabolites and their associated pathways would be valuable in future biotechnology applications of the genus Cymbopogon.