Salinity in soil can affect Jatropha seedling metabolism, interfering with plant establishment. In this study, the effect of salinity on the mobilization of reserves during the development of Jatropha seedlings was tested. Two genotypes of Jatropha were used and three concentrations of NaCl were applied between the 4th and 8th days after germination. The effects of salinity on seedling growth, in terms of fresh and dry phytomass, ionic partition, and sugar quantification, starch, proteins, amino acids, and lipids were evaluated in cotyledon leaves, hypocotyls, and roots. There was an increase in the content of all classes of macromolecules analyzed in at least one of the organs. It is hypothesized that the hypocotyls acted as an accumulating organ of Na+. The accumulations of amino acids and protein in roots suggest that metabolic responses occurred in response to the ionic and osmotic effects of NaCl, although this accumulation did not appear to prevent biomass losses in seedlings. Furthermore, the findings of this study demonstrate that salinity inhibits the mobilization of lipids and carbon stocks from cotyledon leaves to the rest of the plant, and together with the synthesis of proteins and amino acids that occurred primarily in roots, contributed to response of these plants to salinity.