Shifting from chemical-intensive practices to organic-based farming within the rice-wheat rotation (RWR) is crucial for its long-term sustainability. This highly productive system holds a significant carbon (C) sequestration potential if managed efficiently. The dynamics of soil organic-C profoundly impacts the global climate change and crops’ productivity, necessitating the continuous monitoring of organic carbon to ensure soil vitality. Hence, we have evaluated the long-term (twenty-one years) impact of organic amendments on yields of the RWR, soil properties and C-dynamics. After 21 years, we observed that organic-based amendments increased the rice and wheat grain yields by 33.4–52.5% and 20–42.8%, respectively, over the control (no organics). On an average, in top 0.0–0.15 m soil layer, the organic-manured plots had 21.6%, 21.3% and 23.4% greater available nitrogen (N), phosphorous (P) and potassium (K) over the control plot, respectively. Furthermore, such organic-manured plots recorded 32.9–50.8% and 6.04–32.3% greater microbial biomass carbon (MBC) and dehydrogenase activity (DHA) over the control. Also, the use of organic amendments had a significant (p≤0.05) and positive impact on the soil carbon dynamics (0.0–0.45 m). In 0.0–0.45 m soil depth, the organic-manured treatments registered a 25.9–44.2% greater total organic carbon (TOC) than the control. These treatments improved the active (labile, very labile) and recalcitrant (less labile, non-labile)-C pools especially in upper soil layers. In summary, the synergistic use of Sesbania green manure, Leucaena leucocephala leaf manuring, farmyard manure, and biofertilizers (blue-green algae/Azotobacter etc.) proves effective in restoring soil health and enhancing crop productivity by increasing soil organic carbon and ensuring nutrients availability. Thus, these organic amendment treatments can be advocated to farmers to sustain the productivity of the rice-wheat ecosystems. •Organic amendments had significant positive impact on rice (33.4–52.5 %) and wheat (20–42.8 %) yields over the control.•Organic-manured improved the active (labile, very labile) and recalcitrant (less labile, non-labile)-C pools.•Also, the use of organic amendments significantly improved soil microbial properties besides available nutrients.•Organic amendments enhanced the stability for C-sequestration and accessibility of vital plant nutrients