Plants defense responses to abiotic stresses, including salinity stress, involve stimulation of defense related pathways such as biosynthesis of secondary metabolites and induction of endogenous antioxidant enzyme responses. In the present study, a single seed origin clonal line of Swertia chirayita inoculated with Lactobacillus plantarum (LP) was grown under different salinity levels. Control had no LP inoculation. S. chirayita inoculated with LP showed higher accumulation of proline, low proline dehydrogenase activity, up-regulation of pentose phosphate pathway, down-regulation of succinate dehydrogenase activity (Krebs cycle) and low total phenolic content with increased salt concentrations. In comparison, S. chirayita without LP adopted a different biochemical mechanism to counter salt stress (NaCl) by up-regulating both pentose phosphate pathway and Krebs cycle along with stimulation of phenolic biosynthesis. Guaiacol peroxidase (GPX) activity increased with and without LP treatment in response to increasing concentrations of salt. These results indicate that S. chirayita inoculated with LP exhibits a greater salinity stress tolerance than S. chirayita without LP by adopting a more energy efficient defense responses and potentially efficiently partitioning carbon flux between primary and secondary metabolism to counter salt induced oxidative stress.