An experiment was conducted in farm area of Soil Science and Agricultural Chemistry, Birsa Agricultural University, Ranchi, to study the indigenous nutrient supply from nutrient omission plots with and without incorporation of crop residues and their response on partial factor productivity, recoveries and efficiencies of applied nutrients under maize-wheat cropping system. The experiment comprising five treatments with and without crop residues incorporation, replicated four times in a RBD. The results revealed that Partial Factor Productivity of applied N, P & K under maize – wheat cropping system, for SSNM treatment was 37.88 and 35.19, 78.14 and 72.58 & 78.14 and 72.58 kg grain yield per kg N, P and K applied, which was higher than that of NPK treatment (34.57 and 33.01, 60.11 and 57.40 & 62.85 and 60.01 kg grain yield per kg N, P and K applied) with and without incorporation of crop residues, respectively. The agronomic use efficiency of applied N was higher (25.11 - 25.64 kg increase in grain yield per kg applied N) than applied P (24.69 – 27.43 kg increase in grain yield per kg applied P) and followed by applied K (15.77 – 20.34 kg increase in grain yield per kg applied K) in maize-wheat cropping system with and without incorporation of crop residues. With the incorporation of crop residues the nutrient internal use efficiency increased by 3% in wheat but there was not effect of residue incorporation on N internal use efficiency of maize and maize-wheat cropping system. Apparent recovery efficiency of applied N in maize, wheat and maize-wheat cropping system (61.54 – 62.16, 45.97 – 56.87 and 55.64 – 63.15 kg N taken up per kg N applied) was higher than applied P (9.16 – 12.43, 9.58 – 10.45 and 7.83 – 8.57 kg P taken up per kg P applied) and followed by K (84.24 – 89.79, 56.45 – 67.28 and 38.05 – 49.57 kg K taken up per kg K applied).