Rice-based intensive cropping systems require high input levels making them less profitable and vulnerable to the reduced availability of labor and water in Asia. With continuous conventional puddled rice transplanting, the situation is exacerbated by damaged soil structure, declining underground water and decreasing land and water productivity. To minimize these negative effects a range of new crop establishment practices have been developed (zero tillage, dry direct seeding, wet direct seeding, water seeding, strip planting, bed planting, non-puddled transplanting of rice, mechanical transplanting of rice crop and combinations thereof) with varying effects on soil health, crop productivity, resource saving and global warming mitigation potential. Some of these allow Conservation Agriculture (CA) to be practiced in the rice-based mono-, double- and triple cropping systems. Innovations in machinery especially for smallholder farms have supported the adoption of the new establishment techniques. Non-puddling establishment of rice together with increased crop residue retention increased soil organic carbon by 79% and total N (TN) in soil by 62% relative to conventional puddling practice. Rice establishment methods (direct seeding of rice, system of rice intensification and non-puddled transplanting of rice) improve soil health by improving the physical (reduced bulk density, increased porosity, available water content), chemical (increased phosphorus, potassium and sulphur in their available forms) and biological properties (microbiome structure, microbial biomass C and N) of the soil. Even in the first year of its practice, the non-puddled transplanting method of rice establishment and CA practices for other crops increase the productivity of the rice-based cropping systems. Estimates suggest global warming potential (GWP) (the overall net effect) can be reduced by a quarter by replacing conventional puddling of rice by direct-seeded rice in the Indo-Gangetic Plains for the rice-based cropping system. Moreover, non-puddled transplanting of rice saves 35% of the net life cycle greenhouse gases (GHGs) compared with the conventional practice by a combination of decreasing greenhouse gases emissions from soil and increasing soil organic carbon (SOC). Though the system of rice intensification decreases net GHG emission, the practice releases 1.5 times greater N2O due to the increased soil aeration. There is no single rice establishment technology that is superior to others in all circumstances, rather a range of effective technologies that can be applied to different agro-climates, demography and farm typologies.