Iron-biofortification is a sustainable food-based approach to combat iron deficiency by increasing iron content and bioavailability in agronomic crops. Siderophore producing microbes offer a sustainable and low-cost way to increase iron supply in crops. Also, certain substances released from organic amendments act as iron-chelators which increase the solubility as well as the availability of iron to plants. Present study investigated the role of siderophore-producing endophytic bacteria and biochar on iron-fortification of a novel crop quinoa in iron-limited saline conditions. The surface-disinfected seeds of quinoa were inoculated with Burkholderia phytofirmans PsJN (CFU = 109) and sown in saline soil (EC 20 dS m−1) amended with biochar (1% w/w). Results revealed that biochar and PsJN particularly when applied together significantly enhanced plant growth, grain yield, and grain nutrient contents of quinoa. Strikingly, iron concentration in quinoa grains was increased up to 71% by the combined application of biochar and PsJN. Moreover, plant physiological parameters were also improved significantly by the integrated application. However, enzymatic/non-enzymatic antioxidants activities were decreased by integrated treatment thus ameliorated salinity stress. Our study suggests that integrated application of siderophore-producing bacteria and biochar could be a promising, sustainable and cost-effective strategy which is easily integratable into the existing farming practices to achieve food fortification with micronutrients in developing countries.