This study aimed to evaluate the salt stress response of four quinoa (Chenopodium quinoa Willd.) varieties (Q102, Giza 02, Q101, and Black) cultivated in Algeria by assessing a range of physiological and biochemical traits. Specifically, four seed germination traits, seven plant growth parameters, three chlorophyll fractions (total, chlorophyll a, and chlorophyll b), and four non-enzymatic antioxidants (proline, soluble sugars, total phenolics, and saponins) were measured. Salt stress was simulated using seven NaCl concentrations: 0 mM (control), 50 mM, 100 mM, 150 mM, 200 mM, 250 mM, and 300 mM. During the germination phase, the absolute decrease (AD), salt tolerance index (STI), and inhibition index (II) were identified as the most informative indicators for discriminating varietal salt tolerance across treatments. Cluster analysis grouped the varieties into two distinct categories, with Black and Q101 exhibiting the highest germination-stage salt tolerance. At the maturity stage, ANOVA results indicated that root length stress tolerance index (RLSTI), seed polyphenol content, and seed saponin content were the most significant traits associated with both non-enzymatic antioxidant responses and plant growth performance under salt stress. Furthermore, biplot analysis revealed Black as the most salt-tolerant variety under 250 mM NaCl, whereas Giza 02 and Q102 exhibited reduced tolerance. These findings suggest that indices such as germination stress index, RLSTI, and the contents of seed polyphenols and saponins can serve as reliable markers for the selection of salt-tolerant quinoa genotypes.