Conservation agriculture (CA) is inadequately developed for rice-based cropping systems widely practiced in Bangladesh. The current drawback is the implementation of CA for all crops including rice (Oryza sativa L., ecotype ‘transplanted aman’ [T. aman]) to increase rice–wheat (Triticum aestivum L.) rotation productivity. It is important to identify the best combination of tillage types and cropping systems to achieve a high yield of component crops and improve soil health. Three tillage practices, assigned to main experimental plots [namely, zero tillage (ZT), conventional tillage using a rotary tiller (CT) and deep tillage using a chisel plough (DT)] and three different cropping systems, assigned to sub-plots [namely, WFT: wheat–fallow–T. aman, WMT: wheat–mungbean (Vigna radiata L. Wilczek)–T. aman and WDT: wheat–dhaincha (Sesbania rostrata)–T. aman], were tested. After 4 years, ZT under WDT and WMT significantly increased soil organic matter (SOM) at 0–150 mm depth, and these replicates also held the highest levels of total organic carbon. Soil organic carbon (C) increased at a rate of 1.17 and 1.14 t/ha/y in ZT under WDT and WMT, respectively, while CT and DT under WFT were almost unchanged. After 4 years, SOM build-up by the three-crop system (WDT and WMT) under ZT helped conserve soil moisture and improve other soil properties, such as reduction in soil strength and bulk density and increase plant available water content, thus maintaining an optimum soil water infiltration rate. Zero tillage under WMT and WDT showed significant improvements in root mass density of rice and wheat at increased soil depth. The WDT and WMT plots under DT consistently gave the highest yield followed by WDT and WMT under CT, in contrast with ZT under WMT or WDT, which showed the highest improvement in crop yields over the years. In summary, minimum soil disturbance together with incorporation of a legume/green manure crop into the rice–wheat system as well as the retention of their residues increased soil C status, improved soil properties and maximized grain yields.