Quinoa (Chenopodium quinoa Willd.) is a halophytic crop that shows resistance to multiple abiotic stresses, including salinity. In this study we investigated the salinity tolerance mechanisms of six contrasting quinoa cultivars belonging to the coastal region of Chile using agro-physiological parameters (plant height (PH), number of branches/plant (BN), number of panicles/plant (PN), panicle length (PL), biochemical traits (leaf C%, leaf N%, grain protein contents); harvest index and yield (seed yield and plant dry biomass (PDM) under three salinity levels (0, 10, and 20 d Sm−1 NaCl). The yield stability was evaluated through comparision of seed yield characteristics [(static environmental variance (S2) and dynamic Wricke’s ecovalence (W2)]. Results showed that significant variations existed in agro-morphological and yield attributes. With increasing salinity levels, yield contributing parameters (number of panicles and panicle length) decreased. Salt stress reduced the leaf carbon and nitrogen contents. Genotypes Q21, and AMES13761 showed higher seed yield (2.30 t ha−1), more productivity and stability at various salinities as compared to the other genotypes. Salinity reduced seed yield to 44.48% and 60% at lower (10 dS m−1) and higher salinity (20 dS m−1), respectively. Grain protein content was highest in NSL106398 and lowest in Q29 when treated with saline water. Seed yield was positively correlated with PH, TB, HI, and C%. Significant and negative correlations were observed between N%, protein contents and seed yield. PH showed significant positive correlation with APL, HI, C% and C:N ratio. HI displayed positive correlations with C%, N% and protein content., All measured plant traits, except for C:N ratio, responded to salt in a genotype-specific way. Our results indicate that the genotypes (Q21 and AMES13761) proved their suitability under sandy desert soils of Dubai, UAE as they exhibited higher seed yield while NSL106398 showed an higher seed protein content. The present research highlights the need to preserve quinoa biodiversity for a better seedling establishment, survival and stable yield in the sandy desertic UAE environment.