This study was conducted to evaluate influence of zinc (Zn) application on productivity, grain biofortification and grain quality of wheat planted under plough tillage (PT) and zero tillage (ZT) systems. Zn was delivered as soil application (10 kg ha−1), foliage spray (0.025 M) and seed priming (0.5 M) in wheat planted under PT and ZT systems. ZT had higher total soil porosity, total soil organic matter, soil organic carbon and soil microbial biomass carbon than PT. Zn application, by either method, improved grain yield, grain Zn and grain quality in both tillage systems. The grain Zn concentration was 72% and 59% higher with soil-applied Zn in ZT wheat during 2016–2017 and 2017–2018, respectively, compared with no Zn. However, Zn seed priming was the most effective in improving wheat grain yield in both tillage systems. Foliage and Zn soil application were better in improving the indices of Zn use efficiency of Zn. In conclusion, Zn seed priming was the most effective method in improving the wheat grain yield, whereas soil Zn application in ZT and foliar applications in PT were the most effective for grain Zn biofortification. However, Zn soil application was the most cost-effective method of Zn application.