Abstract Jatropha curcas is a common species in Brazil, potentially being an option to produce oil for bioenergetic purposes. Around the world, J . curcas has been cultivated in areas of low fertility, in the presence of salts, and with the use of brackish groundwater. Salt stress can hinder the absorption of nutrients and allow entry of ions in toxic concentrations, affecting the development and productivity of plants. This study aimed to evaluate the effect of salinity on the gaseous exchange and the dynamics of some mineral nutrients in the leaves, stems and roots of J . curcas , subjected to two levels of NaCl (0 and 150 mM) in four genotypes: CNPAE183 (tolerant‐like), JCAL171 (sensitive‐like) and CNPAE133 and CNPAE266 (confused responses to tolerance). Salt treatment promotes a strong reduction in photosynthesis and plant height in all genotypes, although more drastic in CNPAE266 (77.5% and 70% respectively). Additionally, NaCl reduced the content of manganese, calcium, potassium and phosphorus in the leaves, elements linked to gas exchange. The salt‐tolerant‐like (CNPAE183) and salt‐sensitive‐like (JCAL171) transcriptome matched the applied sequences, with few chimeric sequences and novel transcripts with no similarities.