Nutrient use efficiency is reported as a strong indicator of the buildup soil nutrient status for nutritional security of crops through an integrated nutrient management approach under a rice-wheat system. The data revealed that integrated application of manures and fertilizers reported maximum organic carbon (0.39%) in the treatment receiving 100% of the recommended dose of fertilizers (RDF) + farmyard manure and lowering the pH to 6.39. The maximum available N (360.8 kg ha−1) was found in 100% RDF + press mud treatment; available P (66.30 kg ha−1) was found in 75% RDF + poultry manure; and available K, Zn, Cu, and Fe (226.3 kg ha−1 and 2.220, 0.732, and 36.87 mg kg−1, respectively) in 100% RDF + farmyard manure treatments. Similarly, total macro- and micronutrient content in soil increased with the addition of organic manures alone or in combination with chemical fertilizers. The highest agronomic efficiency and utilization efficiency of nitrogen (41.83 and 102.55 kg kg−1, respectively) and phosphorous (83.57 and 204.9 kg kg−1, respectively) were recorded in the treatment receiving 75% RDF + poultry manure. This study concluded that the integrated application of manures and chemical fertilizers is a must for improving soil nutrient status and nutrient use efficiency and ultimately enhances nutritional security under a rice-wheat system.