• Chia plant was more sensitive to salinity during seedling growth stage compared to the germination's one. • During germination, antioxidant enzymes activity increased with increasing salinity up to 200 mM. • At seedling growth, the highest amount of total phenols and flavonoid was achieved at the 40 mM salinity level. • During seedling growth, the highest amount of soluble sugars, nitrogen and protein was obtained at salinity levels less than 40 mM. • Based on Gompertz model's, salinity reduced germination and seedling establishment and increased the time to reach the maximum value of these traits. Salvia hispanica (chia), a genus of Lamiaceae is a super food plant, which could be used as an oilseed and industrial medicinal crop in agro-ecosystems. High salinity inhibits chia seed germination and seedling growth, but the plant is moderately tolerant to salt. It is therefore important to study the role of antioxidant enzymes, biologically active compounds, and other eco-physiological responses related to salinity tolerance in this plant. However, despite of many nutritional benefits, there is a lack of information about chia seeds and seedling eco-physiology. Two experiments were conducted based on the completely randomized design in three replications. In the first experiment, salinity tolerance of chia was evaluated using final germination percentage, mean germination time, germination rate, seedling vigor and antioxidant enzymes activity at germination stage at six levels of sodium chloride (NaCl) solutions including (0, 50, 100, 150, 200, 250 mM). In the second experiment, salinity tolerance of chia seedling were evaluated at seven levels of NaCl solutions up to 150 mM (0, 20, 40, 60, 80, 100 and 150 mM). Results revealed that salinity significantly affected all traits except for seedling water content and photosynthetic water use efficiency at the seedling stage. Among seed germination parameters, only mean germination time increased by 77.2% at 200 mM salinity concentrations compared to control. Seed soluble protein increased by 37.50% at 50 mM NaCl and then declined by at 150 mM 46.36%. The activity of catalase and peroxidase increased 125.5% and 99.4% with increasing NaCl concentration from 150 to 200 mM, but malondialdehyde activity decreased 53.9%. It was revealed that secondary metabolites (total phenol and flavonoids) in chia seedlings increased by 55.0% and 9.9% at 40 mM, NaCl concentration while soluble sugars, nitrogen and protein content declined by 73.0, 57.6 and 57.6% at 150 mM compared to control salinity treatment. In addition, salinity had a negative effect on stomatal conductance, photosynthesis and transpiration rate, which are key players in salinity stress tolerance mechanisms of chia seedlings, especially up to 40 mM salt concentrations. Non-linear gompertz function provided an excellent description for chia seed germination (R 2 adj ≥ 0.97 and RMSE ≤ 4.49) and seedling establishment (R 2 adj ≥ 0.93 and RMSE ≤ 5.41) under salinity condition. A significant reduction in seed vigor index (40.4%) occurred at 50 mM NaCl concentration. chia seedlings below 40 mM NaCl concentration may encounter less detrimental effect.