Salicylic acid (SA) is an effective elicitor for enhancing product formation in various agricultural practices. This study examined the diverse responses to physiological metabolites and the pathway modifications in broad-spectrum resistance-1 (BSR1) of Cajanus cajan after treatment with SA using a metabolomics technique. The significance of the SA function at the metabolite level was examined by treating C. cajan with various concentrations of SA and germinated by soaking in water for different time periods. The secondary metabolites were recovered and investigated by gas chromatography-mass spectrometry for all the periodic conditions. Chemometric analysis of the collected samples showed that the seeds responded to the SA treatment. Acetic acid increased in germinated seeds after the SA treatment. In addition, the up-regulated metabolite production was downregulated in the C. cajan seeds before germination. The levels of metabolites, including hyacinthin, furaneol, citramalic acid, palmitate, stearate, linoleate, tocopherol, glucobrassicin, syringol, and hydroxy acetophenone, were increased after the SA treatment compared to control. Hence, the SA-treated seedling is a potential bio-factory for nutraceutical products to provide significant health benefits to the human population.