However, higher SOC content of 8.14 g kg-1 of soil was found in reduced tilled residue retained plots followed by 10.34 g kg-1 in furrow irrigated raised beds with residue retained plots. Whereas, the lowest level of SOC content of 5.49 g kg-1 of soil were found in puddled transplanted rice followed by wheat planted under conventionally tilled plots. Average SOC concentration of the control treatment was 0.54%, which increased to 0.65% in the RDF treatment and 0.82% in the RDF+FYM treatment. Compared to F1 control treatment the RDF+FYM treatment sequestered 0.33 Mg C ha-1 yr1 whereas the NPK treatment sequestered 0.16 Mg C ha-1 yr-1. Long term conservation tillage significantly increased 66.1%, 57.9%, 50.9%, 38.3%, 37.3% and 32% LFOC, SOC, PON, TN, LFON, DOC and POC, over conventional tillage (T7) treatment and WSC 39.6% in surface soil and 37.4% in subsurface soil. Under RWCS, TOC contents were similar in 50% RDN as CF+50% RDN as GM/SPM (F6) and1/3rd N as CF+1/3rd N as FYM+1/3rd N as GM/SPM (F7) and 75% RDN as CF+25% RDN as FYM (F3) plots and significantly higher than those in control (no manure and fertilizer) (F1) plots (by 50.4% 48.3%, and 43.3% respectively). Manure addition further enhanced TOC contents, which were highest following the 50% RDN as CF+50% RDN as FYM (F5) treatment (21.37 gkg−1). Therefore, conservation agriculture in rice-wheat system can help directly in building–up of soil organic carbon, labile organic carbon fractions and improve the fertility status of soil.