Salt tolerance is a much-needed potential in cereal crops. To date, numerous research protocols have focused on establishing selection programs to increase tolerance and productivity of crops in salt-stressed areas. In this study, we aimed to induce callus from endosperm-supported mature embryos of five common wheat varieties (Nassim, Wissam, Wafia, Rajae, and Tigre) subject directly to various increasing NaCl concentrations (0–9 g/L) under in vitro culture process. We chose callus growth, organic solutes accumulation, and ion content as main traits to evaluate the impact of salinity on stressed calli. Our findings indicate that the accentuated salinity pressure leads to a substantial elevation of Cl−, Na+, proline and soluble carbohydrates content, along with a reduction in callus growth, potassium accumulation, and K+/Na+ ratio. Yet, the performance under salt stress was significantly dependent on the varietal effect. At the highest concentration, the marked values of these solutes (12.06 µmol/g FM of proline; 43 µmol/g FM of Total soluble sugar; 31.15 mg/ g DM Na+; 12.82 mg/g DM of Cl−, 12.61 mg/g DM of K+ and 0.40 K+/Na+) were respectively recorded by Rajae. Principal component analysis (PCA) first classified Rajae as the most tolerant followed by wafia as tolerant, while Wissam and Tigre were ranked as sensitive. Whereas, the variety Nassim showed a moderate tolerance. Besides the K+/Na + Ratio and salinity tolerance index (STI), the PCA analysis has shown that all the studied physiological criteria seem worthwhile for better discrimination of the varieties tested according to their reaction to salinity.