Iron (Fe) deficiency is a major health issue worldwide, which can be alleviated by biofortification. Agronomic biofortification is a practical solution to overcome the Fe deficiency in cereals without sacrificing on yield. This study was carried out to evaluate the effect of Fe application on productivity, grain biofortification, and grain quality of bread wheat under conventional and conservation production systems. The experiment was laid out in randomized complete block design (RCBD) with split-plot arrangement where wheat was sown under conventional tillage (CT) and zero tillage (ZT) systems and Fe was applied through various methods (no Fe application, seed priming (0.3% Fe solution), seed coating (250 mg kg−1 seed), basal application (12 kg ha−1), and foliar spray (0.5% Fe solution)). Iron nutrition significantly enhanced the yield and related traits and grain fat and protein contents. Averaged across two years, grain yield improvement from different Fe application methods was in the order of seed priming>basal application>foliar application>seed coating with respective increase of 33%, 28%, 25%, and 21% relative to control treatment. Grain Fe concentration was 65% and 58% higher with Fe foliar application compared with control during 2017–2018 and 2018–2019. Interaction of tillage systems and Fe nutrition highlighted that 1000-grain weight and grain yield were improved, whereas Fe seed priming in ZT system provided maximum 1000-grain weight and grain yield. The Fe application through either method proved to be profitable and the highest benefit-cost ratio was obtained with Fe foliar application. Among tillage systems, the highest net benefits were obtained with ZT. Zero tillage significantly improved the soil microbial biomass carbon, soil microbial biomass nitrogen, and soil organic carbon by 9.25%, 2.5%, and 14%, respectively, compared with CT. In conclusion, Fe seed priming in both tillage systems improved the yield, and proved to be the most cost-effective, whereas foliar application improved the grain Fe concentration in both tillage systems.