A field experiment was conducted during rainy seasons of 2003-04 and 2004-05. Fourteen treatments consisting of two fertility levels (50% and 100% recommonded NPK) and their combination with FYM and supplementary nutrients viz. boron and iron besides control were tested in randomized block design with three replications. The results revealed that soybean yield attributed to cumulative effect of yield attributes viz., pods/ plant, seeds/pod and hundred seed weight were increased significantly by the addition of micronutrients and FYM at both the fertility levels (50% and 100% NPK). Integrated use of FYM (10.0 t/ha) and micronutrients viz., boron (2.0 kg/ha) and iron (5.0 kg/ha) with inorganic NPK can replace upto 10 kg N, 30 kg P2O5 and 20 kg K2O/ha. Mean relative growth rate (RGR) and net assimilation rate (NAR) and leaf area index (LAI) were significantly affected by supplementation of inorganics (50% and 100% NPK) with FYM and/or micronutrients viz., boron and iron. Application of FYM, boron and iron along with inorganic fertilizer (50% and 100% recommended NPK) also significantly increased the root dry biomass, number of nodules, dry weight/plant and leghaemoglobin content at 60 days stage. Net returns and benefit: cost ratio was highest where boron (2.0 kg/ha) was applied with 100 % NPK and lowest in control (Inoculated). Highest protein and oil content and yield were recorded with RDF + FYM. Application of FYM, Fe and B with both 50 and 100% recommended fertilizers (RDF) markedly improved the content of unsaturated fatty acids (linolenic, linoleic and oleic) and reduced the content of saturated fatty acids (palmatic and stearic). Use of organic sources and micronutrients helped in maintaining soil fertility in terms of available nutrients and fertility balance. It was concluded that application of FYM and micronutrients viz., Fe and B along with 100 % NPK was essential for higher productivity and profitability of soybean as well as maintaining soil fertility.