A long-term field experiment was conducted under rainfed conditions at the research farm of Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India, to assess the long-term effects of inorganic and organic fertilizer applications on crop yield and soil carbon dynamics in a rice-lentil cropping system. The 12-year study (2005-2017) was laid out in a randomized block design with eight treatments comprising different combinations of inorganic fertilizers and farmyard manure (FYM), applied to rice during the kharif season and lentil during the rabi season. The objective was to evaluate the influence of these nutrient management practices on crop productivity, soil organic carbon (SOC), soil microbial carbon, and their potential for carbon sequestration. Results indicated that full i.e. 100% replacement and partial substitution (50%) of chemical nitrogen (50% N) with FYM, as well as the combined application of FYM and inorganic fertilizers, significantly enhanced rice yield compared to only chemical fertilizer application. Higher nutrient input levels led to greater improvements in crop yield and SOC accumulation. A strong positive correlation was observed among crop yield, SOC, and soil microbial carbon content (SMC), highlighting that integrated nutrient management practices enhance both soil carbon sequestration and system productivity. The study concludes that the combined use of organic and inorganic fertilizers is a sustainable strategy for maintaining soil health and improving productivity in rainfed rice-lentil systems.