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Plants thrive under abiotic and biotic stress conditions with the changes in phytohormones like salicylic acid (SA), resulting in the synthesis of secondary metabolites. The present study determines the response of plants in producing secondary metabolites towards different SA concentrations at varying time intervals. Liquid chromatography-mass spectrometry-based metabolomics studies in Aphanamixis polystachya (Wall.) Parker seedlings are grown at 10 mM, 50 mM, and 100 mM SA concentrations, showed the differential expression of metabolites towards the stress. Alkaloids like amaranthin showed a 15-fold increase on the second day, and analog of androvinblastin showed a 20-fold increase on the sixth day in 10 mM SA compared with other groups. Flavanoid cyanidin 3-3 glucosyl was found to be with a 22-fold increment along with terpenoids betavulgaroside (18-fold), asiaticoside (17-fold), mubenin B (20-fold), and deslanoside (22-fold) increment in 50 mM SA on the sixth day. The shock exerted by 100 mM was too harsh, and the lowered metabolite production level was insufficient for the seedlings to survive at this higher SA condition. Arrangement of stressed groups using Pearson correlation studies, principal component analysis, and partial least square analysis placed 10 mM SA and controlled group closer and 50 mM SA and 100 mM SA groups closer to each other. The study observed that SA regulates metabolites that mediate biotic stress responses at low concentrations, and higher concentrations regulate abiotic stress regulating metabolites.