Quinoa’s exceptional capacity to tolerate high salt levels presents a promising solution to the agricultural challenges posed by salt stress. This study aimed to explore salt stress effects on three quinoa accessions (18 GR, R-132, and DE-1) and to compare the influence of greenhouse and field growing conditions on their salinity tolerance. The plants were irrigated by 50, 100, 150, and 200 mM NaCl concentrations. The results showed that quinoa plants’ response to morphological, physiological, biochemical, and enzymatic parameters was influenced by NaCl concentration, accession, growing conditions, and their interactions. As salinity irrigation increased, aerial part length and leaf area decreased significantly (p < 0.05) for all studied accessions, correlating with plant photosynthetic parameters. Greenhouse conditions promote faster and more vigorous growth with a larger leaf area compared to field cultivation. Furthermore, at 200 mM concentration, the DE-1 accession displayed greater photosynthetic activity, recording values of 195.66 ± 3.56 and 120 ± 1.13 µmol·m−2·s−1 for greenhouse and open field conditions, respectively. NaCl stimulated MDA and H2O2 in both conditions for all accessions, and the DE-1 accession displayed the lowest levels. Proteins, sugars, proline, peroxidase, ascorbate peroxidase, and catalase were stimulated by salt stress, except in the R-132 accession. Field cultivation resulted in a more severe salinity response. Greenhouse conditions may enhance quinoa’s salt tolerance due to the less demanding growth conditions. DE-1 exhibited the highest salt tolerance, while R-132 showed the lowest. This study sets the stage for further research into the genetic basis of salt tolerance in various quinoa accessions, optimizing growth in salty regions through farming practices, and confirming the obtained results in real-world conditions for sustainable agriculture.