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Main conclusion Growth was not strictly linked to photosynthesis performance under salinity conditions in quinoa. Other key traits, which were varieties-specific, rather than photosynthesis explained better growth performance. Abstract Phenotyping for salinity stress tolerance in quinoa is of great interest to select traits contributing to overall salinity tolerance and to understand the response mechanisms to salinity at a whole plant level. The objective of this work was to dissect the responses of specific traits and analyse relations between these traits to better understand growth response under salinity conditions in quinoa. Growth response to salinity was mostly related to differences in basal values of biomass, being reduced the most in plants with higher basal biomass. Regarding the relationship between growth and specific traits, in Puno variety, better photosynthetic performance was related to a better maintenance of growth. Nevertheless, in the rest of the varieties other traits rather than photosynthesis could better explain growth response. In this way, the development of succulence in F-16 and Collana varieties, also the osmotic adjustment but in smaller dimensions in Pasankalla, Marisma and S-15-15 helped to maintain better growth. Besides, smaller increases of Cl− could have caused a limited nitrate uptake reducing more growth in Vikinga. Ascorbate was considered a key trait as a noticeable fall of it was also related to higher reductions in growth in Titicaca. These results suggest that, due to the genetic variability of quinoa and the complexity of salinity tolerance, no unique and specific traits should be taken into consideration when using phenotyping for analysing salinity tolerance in quinoa.