We measured the long-term (28 years) sustainability of rice-wheat cropping system under integrated nutrient management practices emphasizing the trends in grain yields, sustainable yield index (SYI) and nutrient budgeting. The data of long-term experiment revealed that grain yield of both rice and wheat declined under control and sub-optimal fertilizer inputs (50% or 75% recommended fertilizer NPK). Negative yield trend (slope) was observed in control plots for rice (–0.0296) and wheat (–0.0070); whereas positive yield trend was observed under treatments receiving organic supplements. The SYI values indicate that rice yields are more sustainable than wheat. Data on apparent nutrient balance showed a deficit of N (–42.2 kg/ha/year), P (–9.1 kg/ha/year) and K (–52.2 kg/ha/year) under control plots. Surprisingly, there was net depletion of K under the organic supplemented plots. Correlation study revealed that apparent balance of K was negatively correlated with SYI (r = –0.921 for rice; r = –0.914 for wheat) and yield slope (r = –0.870 for rice; r = –0.896 for wheat). If the trend of K imbalance is not reversed, the potential to improve N and P fertilizer use efficiency and crop yields will be limited.