Zinc (Zn) deficiency in rotations of rice (Oryza sativa L.) and wheat (Triticum aestivum L.) impedes the productivity of both component crops. Fertilisation with Zn and switching to conservation tillage systems may help to improve soil health and the productivity of both rice and wheat. However, it is not clear whether, in conservation tillage systems, Zn application to either crop will fulfil the requirement of the following crop through a residual effect. This study was designed to evaluate the influence of Zn applied to wheat on the performance of rice under conventional (puddled transplanted rice, PuTR) and conservation (direct-seeded aerobic rice, DSAR) tillage. As a part of a long-term experiment, Zn was applied as foliage spray (FA, 0.025 M), by seed priming (SP, 0.5 M) and by soil application (SA, 10 kg ha^–1) in plough-till wheat (PTW) and no-till wheat (NTW). Controls without Zn application were included (PTW-C, NTW-C). After wheat harvest, rice was planted as PuTR and DSAR in each of the eight Zn application × wheat tillage treatment combinations. Compared with PuTR, DSAR significantly improved soil fertility (nitrogen, phosphorus, Zn), soil organic matter (1.5–4.5%), soil organic carbon (3%), soil microbial biomass carbon (2.5%) and grain yield (5.6%). Overall, DSAR preceded by NTW had higher soil organic carbon (4.3%), soil microbial biomass nitrogen (1.6%) and soil microbial biomass carbon (3.7%) than PuTR sown after either PTW or NTW. Residual Zn enhanced grain Zn concentration by 15% in rice planted after PTW-SA and 12% after NTW-SA. Overall order of improvement in rice-grain Zn concentration was PTW-SA = NTW-SA > NTW-C = NTW-SP. Likewise, higher grain yield with residual Zn availability was in the order DSAR-NTW-SA > PuTR-PTW-SA during 2018. Highest economic return with high benefit : cost ratio was recorded for DSAR-NTW-SA. Zinc application to the wheat crop effectively improved crop performance and grain quality of the following rice crop in both conventional and conservation tillage systems. However, the conservation system DSAR-NTW-SA may be chosen for improved soil health, and for increased harvest grain yield with better grain quality.