Rice–wheat cropping systems feed millions of people in South and East Asia. However, cereal-based foods are inherently deficient in micronutrients. A strategy involving green manuring and elemental sulfur (S) fertilisation is an innovative approach for biofortification by enhancing bioavailability of micronutrients. We conducted an experiment with a basmati rice (Oryza sativa L.)–durum wheat (Triticum durum Desf.) cropping system that comprised main plot treatments of two green manure crops, Sesbania aculeata Pers. (prickly sesban) and Crotalaria juncea L. (sunhemp), and a fallow. Sulfur as bentonite-S (90% S) was applied in subplot treatments of 20 or 40 kg S ha⁻¹ to rice, 20 or 40 kg S ha⁻¹ to wheat, and 20 or 40 kg S ha⁻¹ to both rice and wheat, with a control (no S fertilisation). There were three replications in a split-plot design. Results showed that micronutrient concentrations and their uptake were in the order iron (Fe) > manganese (Mn) > zinc (Zn) > copper (Cu) in both grains and straw of basmati rice and durum wheat. Compared with fallow, sunhemp green manuring increased Zn and Mn by 11%, Fe by 18% and Cu by 17% in basmati rice grain, and Zn by 21%, Mn by 8%, Fe by 12% and Cu by 8% in durum wheat grain. Compared with the no-S control, fertilisation at 40 kg S ha⁻¹ to both rice and wheat increased Zn by 30%, Fe by 33%, Cu by 23% and Mn by 24% in basmati rice grain, as well as rice grain yield by 10%. The same treatment increased Zn by 42%, Fe by 27%, Cu by 9% and Mn by 18% in durum wheat grain, as well as wheat grain yield by 26%. Thus, green manuring and addition of 40 kg S ha⁻¹ to both rotation crops is an effective strategy to ensure biofortification.