Nutrient budgeting is an useful tool to understand the present and future productivity in relation to land management as well as undesirable effects of nutrient mining and development of toxicities. Long-term experiment conducted on permanent plots for 25 years with rice–rice cropping system at PJTSAU, Rajendranagar indicated that inclusion of manures at both 50% and 25% N substitution during kharif substantially reduced net negative balance when compared to application of chemical fertilizers alone. Nutrient removal over 25 years of experimentation was high in the treatments where in 100% recommend dose of fertilizers were applied through chemical fertilizers and also in treatments where 25% or 50% of N is substituted for with gliricidia green leaf manure. Of the total applied nitrogen through different sources, about 24 to 37.5% nitrogen was recovered by the rice crop in various treatments, gaseous losses were accounted to 12-13% and about 26 to 39.9% of nitrogen was subjected to leaching losses. The positive P balance was ranging from 6.6 to 824 kg ha-1 over 25 years in different treatments. Nitrogen substitution through paddy straw maintained lower negative balance of potassium over FYM, glyricidia substituted treatments or with application of 100% RDF.