The crop productivity in calcareous soils is low due to their low organic matter content, high pH levels and improper nutrient management without considering the indigenous nutrient supplying capacity and crop yield potential; therefore, this study was conducted for a quantitative assessment of the nutrient supplying capacity of a calcareous soil on the productivity of hybrid and conventional rice and maize crops using an omission plot technique. The treatments included the ample application of Nitrogen (N), Phosphorus (P), Potassium (K), Sulphur (S) and Zinc (Zn), and an unfertilized check and omissions of N, P, K, S and Zn in rice and maize for six cropping seasons. The impact of the nutrient omission towards crop productivity was highest for nitrogen followed by phosphorous, potassium, zinc and sulphur. The total grain yield (3 yr average) in the hybrid rice–maize system was highest (16.32 t ha−1) for the optimum fertilized plot and lowest (6.34 t ha−1) for the unfertilized check. The sustainable yield index indicated that hybrid and conventional rice-maize cropping systems were more sustainable in the amply fertilized plot than in the nutrient-limited and unfertilized treatment plots. The average percent contributions of nitrogen, phosphorous, and potassium from the soil towards total nutrient removal were 36, 80 and 137 kg ha−1, in the hybrid system and 24, 54 and 104 kg ha−1 in the conventional system, respectively. The return on investment (ROI) of the N, P, K, S and Zn for the hybrid rice was 21.2, 7.1, 6.7, 4.1, and 0.3 USD, respectively, while for the maize it was 28.8, 7.6, 4.9, 6.5, and 0.7 USD, respectively. The results suggest that there is a direct link between the soil nutrient supplying capacity and the nutrient requirements by different types of crops in calcareous soil; therefore, the omission plot technique used for the assessment of the indigenous nutrient supplying capacity could be used in the larger domain for improved nutrient management, through synchronization with a targeted crop yield for improved productivity, soil fertility, nutrient use efficiency and farm income.