Climate-smart agriculture (CSA) practices are becoming increasingly important due to their better adaptability to harsh climatic conditions (in general) and the unpredictability of monsoons in India (in particular). Conventional rice cultivation (e.g., PTR) involves intensive tilling followed by intensive puddling in standing water that destroys the soil aggregation and depletes carbon pools. Therefore, alternative crop establishment methods need to be devised for the sustainability of system productivity, and the suitabilities of potential oilseeds and pulses need to be tested for cropping intensification in rice-fallow regions. Hence, an ongoing experiment (implemented in 2016) was evaluated to identify the appropriate CSA management practices in restoring soil C and physical health under diversified cropping systems in the rice-fallow system of eastern India. Six tillage and crop establishment methods along with residue management were kept as the main plots [zero-till-direct-seeded rice (ZTDSR), conventional-till-DSR (CT-DSR), puddled transplanted rice (PTR), ZTDSR with rice residue retentions (ZTDSRR+), CTDSR with rice residue retention (CTDSRR+), PTR with rice residue retention (PTRR+)] while five winter/post-rainy crops (oilseeds and pulses) were raised in a subplot. In the ZTDSRR+ production system, soil macro-aggregate (%), macro-aggregate-associated C, MWD, and GMD of aggregates increased by 60.1, 71.3, 42.1, and 17.1%, respectively, in comparison to conventional tillage practices (PTR). The carbon management index (CMI) was 58% more in the ZTDSRR+ production system compared to PTR. Among the winter crops, chickpeas recorded higher values of soil structural indices and C content. In the PTR production system, system productivity, in terms of rice equivalent yield, was comparable to ZTDSRR+. ZT with residue retention in rice followed by post-rainy/winter pulses led to higher C content and structural stability of the soil. Thus, CSA management practices can improve the crop productivity as well as soil health of rice-fallow production systems of eastern India and comparable agroecotypes of South Asia.