Salinity is a major issue affecting photosynthesis and crop production worldwide. High salinity induces both osmotic and ionic stress in plant tissues as a result of complex interactions among morphological, physiological, and biochemical processes. Salinity, in turn, can provoke inactivation of some enzymes in the Calvin-Benson cycle and therefore affect the fine adjustment of electron transport in photosystem I and carbon related reactions. Here, we used three contrasting Jatropha curcas genotypes namely CNPAE183 (considered tolerant to salinity), CNPAE218 (sensible), and JCAL171 (intermediate) to understand salinity responses. By performing a long-term (12 months) experiment in land conditions, we investigated distinct mechanisms used by J. curcas to cope with threatening salinity effects by analyzing gas exchange, mineral nutrition and metabolic responses. First, our results highlighted the plasticity of stomatal development and density in J. curcas under salt stress. It also demonstrated that the CNPAE183 presented higher salt-tolerance whereas CNPAE218 displayed a more sensitive salt-tolerance response. Our results also revealed that both tolerance and sensitivity to salinity were connected with an extensive metabolite reprogramming in the Calvin-Benson cycle and Tricarboxylic Acid cycle intermediates with significant changes in amino acids and organic acids. Collectively, these results indicate that the CNPAE183 and CNPAE218 genotypes demonstrated certain characteristics of salt-tolerant-like and salt-sensitive-like genotypes, respectively. Overall, our results highlight the significance of metabolites associated with salt responses and further provide a useful selection criterion in during screening for salt tolerance in J. curcas in breeding programmes.