Seeds germination and seedlings growth of Cucumis sativus and Solanum lycopersicum were monitored in in vitro and in vivo experiments after application of different concentrations of NaCl (25, 50, 100 and 200 mM). Photosynthetic pigments content and the biochemical responses of C. sativus and S. lycopersicum were assessed. Salinity stress slightly delayed the seeds germination rate and significantly reduced the percentage of germination as well as shoot length under the highest salt concentration (200 mM) in cucumber. Furthermore, root length was decreased significantly in all treatments. Whereas, in tomato, a prominent delay in seeds germination rate, the germination percentage and seedlings growth (shoot and root lengths) were significantly influenced under all concentrations of NaCl. Fresh and dry weights were reduced prominently in tomato compared to cucumber. Photosynthetic pigments content was reduced but with pronounced decreasing in tomato compared to cucumber. Secondary metabolites profiling in both plants under stress was varied from tomato to cucumber. The content of saponins, proline and total antioxidant capacity was reduced more prominently in tomato as compared to cucumber. On the other hand, the content of phenolics and flavonoids was increased in both plants with pronounced increase in tomato particularly under the highest level of salinity stress. The metabolomic profiling in stressful plants was significantly influenced by salinity stress and some bioactive secondary metabolites was enhanced in both cucumber and tomato plants. The enhancement of secondary metabolites under salinity stress may explain the tolerance and sensitivity of cucumber and tomato under salinity stress. The metabolomic evaluation combined with multivariate data analysis revealed a similar mechanism of action of plants to mediate stress, with variant level of this response in both plant species. Based on these results, the effect of salinity stress on seeds germination, seedlings growth and metabolomic content of plants was discussed in terms of tolerance and sensitivity of plants to salinity stress.