Abstract The conservation agriculture (CA) based rice-wheat cropping systems in South Asia can help in enhancing nutrient cycling, soil health and protecting the environment to enhance agricultural ecosystems' sustainability. This study was conducted with four rice establishment methods in main plots comprising (1) zero till dry seeded rice (ZTDSR), (2) conventional till dry seeded rice (CTDSR), (3) Zero till machine transplanted rice (ZTMTR) and (4) conventional puddled manual transplanted rice (PTR). The wheat establishment methods in sub plots comprised (1) conventional tillage with rice straw removed (CTW-R), (2) zero tillage with rice straw removed (ZTW-R) and (3) zero tillage with rice straw retained as surface mulch (ZTW + R). Data showed a significant increase in micro-nutrients fractions and crop yield due to the ZTDSR in rice and ZTW + R in wheat as compared to the conventional tillage practices. Among different fractions, crystalline Fe bound followed by organically bound and amorphous Fe were the dominant fractions in earthworm cast soil under ZTW + R compared with CTW-R. Among different Zn, Fe and Mn fraction, crystalline Fe bound fraction was 18.2 and 2.21% higher in ZTDSR than PTR respectively, where as 56.3% higher under PTR than ZT-DSR for Fe fraction. Under wheat establishment methods, crystalline Fe bound fraction of Zn, Fe and Mn were 19.9, 18.2 and 6.6% higher in ZT + R compared with CT-R in earthworm cast soil. These results highlighted the significance of earthworm activity in earthworm cast soils on micro-nutrients' management through robust interventions for long-term sustainability of CA- based cropping systems.