Modifications in growing techniques can affect the yield and nutritional quality of various cultivated plant species. Owing to its high nutritional value, sweet pepper (Capsicum annuum L.) was used in this study as a model plant to investigate the effect of abiotic stress (Electrical conductivity [EC]) and elicitor (Salicylic acid [SA]) on yield and fruit quality parameters under conditions of greenhouse. Nonetheless, the application of elicitors, are stable molecules that induce the activation of transduction cascades and hormonal pathways, which trigger induced resistance to environmental stress. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence. The aim was evaluated the endogenous H₂O₂ production caused by the effect of different concentrations of (SA) in Capsicum annuum L. in production after elicitation in seedling, and the production of secondary metabolites using GC-MS (flavonoids, tannins and phenolic content as well as the antioxidant properties) in plant and fruit of Capsicum annuum L. to relate their response in metabolic pathways. Results displayed that the use SA, induced an endogenous H₂O₂ and enzymatic activities related with plant defense as phenylalanine ammonia lyase and catalase. This production showed results that could be an indicator for determining application opportunity uses in agriculture for maintaining plant alert systems against a stress. These results were correlated with those obtained from cultivation of capsicum annum until obtaining the fruit at ripe stage had a high content of bioactive compounds that exhibited significant antioxidant properties. The correlation of the contents of flavonoids, tannins and total phenolics and the ability to remove free radicals of the sweet pepper was significant (r = 0.99, P <0.000) in treatment 3 (0.1 mM SA/36 dS/m EC) showed a correlation between the DPPH and ABTS compared with the control. The analysis revealed that significant increased activity of CAT and PAL and H2O2 endogenous were significantly (p < 0.05) perturbed in the stress-induced treatments: in some metabolic pathways as aminoacyl t-RNA biosynthesis.