Long-term application of fertilizer and manure can affect soil properties with implications on the productivity and sustainability of crops. Data from a long-term fertilizer experiment at Bhubaneswar, India was used to study the impact of seven treatments viz. control, application of recommended dose of NPK (NPK), 150% NPK (1.5 NPK), NPK + Zn (NPKZn), NPK + FYM (NPKFM), NPK + Zn + B (NPKZnB) and NPK + Zn + S (NPKZnS) on productivity, sustainability (in terms of sustainable yield index (SYI)), soil properties (physical, chemical and biological) and soil organic carbon (SOC) sequestration of rice-rice cropping system. Results revealed that application of NPKFYM improved the average grain yield and SYI of wet and dry season rice and the system by 36.3, 21.6, and 28.3% and 28.8, 17.1, 22.8%, respectively, over NPK alone. Application of NPKFYM improved soil fertility by stimulating microbial activity, improving soil physical health, resisting drop in pH to more acidity and improving CEC and macro- and micro-nutrients levels. NPKFYM also sequestered higher SOC than NPK alone. Therefore, application of NPKFYM can be recommended for sustaining the productivity of the rice-rice system with improvement of soil health under Inceptisols of Eastern India.