Context Soil salinity is a serious environmental issue that is drastically reducing crop productivity via limiting the uptake of important micronutrients including iron (Fe) and zinc (Zn). Aims To identify the wheat genotypes with better Fe and Zn uptake potential under saline conditions. Methods The seedlings of eight wheat genotypes (SARC-1, SARC-2, SARC-3, SARC-4, SARC-5, SARC-6, SARC-7 and SARC-8) were exposed to salinity (100 mM NaCl), deficiency of Fe and Zn (one-fourth of the control) and their combination of salinity and deficiency of Fe and Zn, created usingHoagland’s nutrient solution for 28 days. Key Results It was noticed that root and shoot growth of all the genotypes decreased due to salinity and nutrient (Fe and Zn) deficiency, and even higher in their combined treatment. The concentration of Na increased while K decreased under both salinity alone and it's combination with nutrient deficiency. The concentrations and uptake of Fe and Zn greatly decreased in the combinedapplication of salinity and nutrient deficiency followed by nutrient deficiency and saline treatments. Multivariate analysis showed that Na uptake was the major reason for the limited growth and nutrient uptake by wheat genotypes. Conclusions SARC-5 was the most sensitive genotype against salinity and nutrient deficiency. In contrast, SARC-1 was the most tolerant genotype against salinity, whichaccumulated the highest contents of both Fe and Zn. Among the eight genotypes used in the present study, SARC-1 is the most suitable genotype for cultivation on Zn and Fe deficient saline soils. Implications The obtained results would be very helpful for ensuring food security and quality in salt affected areas.