Numerous Tunisian arid and semi-arid regions are subjected to soil salinity. Thus, they are known for halophytes plants cultivation, including date palms. Phoenix dactylifera L., cv. ‘Deglet Nour’, is a valuable Tunisian cultivar subjected to high salinity levels. In this way, our purpose is to evaluate the response of its roots to long period exposition to increasing salt concentrations. We started by studying the effects of 4 g/L, 8 g/L, 12 g/L, and 16 g/L NaCl on the parameters of germination (Growth rate—GR, Seed Mortality Rate—SLM, Germination Mean Time—GMT, and Germination Speed—GS) of date palm seeds for a 2-month period. We found that 4 g/L NaCl did not affect the seeds germination, and, hereinafter, the parameters of germination and the radicle length decreased with the increase of NaCl concentrations and experiment time. Then, we demonstrated a high antioxidative enzymes CAT and SOD production in case of salt stress augmentation. Lastly, a metabolomic approach was carried out by LC-HRMS, followed by an untargeted and targeted analysis using the XCMS online and MZmine tools, respectively. The roots chemical composition was compared using PCA. We identified 25 secondary metabolites, divided into 3 categories. Metabolites known for their role in salt stress alleviation include δ-tocotrienol, metabolites identified in salt stress for the first time, and other unknown metabolites.