Abstract Beauty leaf tree (BLT) has been ranked as a valuable 2nd generation feedstock for biodiesel production. This tree is suitable for growing on marginal land to avoid food vs fuel debate. However, at present little is known about its tolerance to marginal soil conditions such as salinity. Thus, a sand culture experiment was conducted, and the seedlings of BLT were exposed to 0, 25, 50, 75 and 100 mM NaCl for up to 245 days. Plant growth and physiological measurements were recorded and the whole leaf and powdered stem were scanned using FTIR-ATR to test if these spectra can be used to delineate differences between the control and the NaCl-treated plants. Results showed that the chlorophyll content and leaf expansion rate were little affected at 25 and 50 mM NaCl, as compared to the control, and they declined at higher NaCl concentrations. The tissue Na and Cl concentrations increased with NaCl increment. The differences between the control and the NaCl-treated plants were distinct at certain FTIR-ATR spectra showing that the plants that were exposed to NaCl had synthesised certain organic compounds to maintain osmotic gradient between the tissues and soil solution. This study found that the biochemical changes that occur in the functional groups of NaCl–treated plants can be detected by the FTIR-ATR spectroscopy, thus showing the potential of this technology to screen large number of genotypes in plant breeding trials. This technology is particularly suited to tree crops that have slow growth rate in the seedling stage.