The involvement of glutathione transferases (GSTs) in plant’s tolerance to abiotic stresses has been extensively studied; however, the metabolic changes occurring in the plants with altered GSTs expression have not been studied in detail. We have previously demonstrated that GmGSTU4 overexpression in tobacco plants conferred increased tolerance to herbicides, partly through its peroxidase activity. Here, we investigated GmGSTU4 transcriptional response to abiotic and chemical stimuli in soybean. Transgenic tobacco plants overexpressing GmGSTU4 were also evaluated regarding their phenotypic and metabolomics responses under salt stress. GmGSTU4 expression was highly induced after salt stress and atrazine treatment. Tobacco plants overexpressing GmGSTU4 were highly tolerant to 150 mM NaCl in vitro. Metabolomics comparison of plants growing under optimal conditions, indicating a shift of the transgenic plants metabolism towards the metabolic profiles observed under stress, increased concentration of precursors of glutathione biosynthesis and hexose concentration reduction. Under salt stress, transgenic plants maintained their cellular homeostasis in contrast to wild-type plants which exhibited deregulated energy metabolism. The metabolic response of the transgenic plants was characterized by higher concentration of protective metabolites such as proline and trehalose and greater induction of the oxidative pentose phosphate pathway. These results confirm GmGSTU4 contribution to salt stress tolerance, and outline a regulatory role that primes plants towards the up-regulation of protective and detoxification mechanisms under abiotic stress.