Over centuries and even today, traditional farming practices are well performed without any ecological degradation. However, management practice such as conservative tillage combined with nutrient and residue could increase the crop production as well as soil fertility. A three-year replicated study was conducted to assess the effects of agronomic modification of traditional farming practices on productivity and sustainability of rice (wet season)-rice (dry season) system (RRS). The replacement of farmers practice (T 2 ) with conservation effective tillage (no-till (NT)) and integrated nutrient management (INM) practice along with 30% residue retention (T 5 ) enhanced the straw, root and biomass yield of both wet season rice (WR), dry season rice (DR) and system as a whole over T 2 . Treatment T 5 recorded significantly lower soil bulk density ( b ) and higher pH than the T 2 after three years of the experiment. Further, treatment T 5 increased total soil organic carbon (2.8%), total soil organic carbon stock (2.8%), carbon sequestration rate (336.5 kg ha −1 year −1 ), cumulative carbon stock (142.9%) and carbon retention efficiency (141.0%) over T 2 of 0-20 cm depth after three year. The soil microbial biomass carbon concentration was significantly the highest under T 5 . Similarly, the dehydrogenase activity was the maximum under T 5 . Adoption of conservation tillage and nutrient management practice involving NT and INM along with residue retention can enhance the system productivity, and C and N sequestration in paddy soils is thereby contributing to the sustainability of the RRS.