Integrated use of bio-organic and inorganic fertilizers can improve crop productivity and sustain soil health and fertility. The present research was conducted for two years at Block Seed Farm, Nabagram, Murshidabad, West Bengal to study the effects of green manuring (GM) with dhaincha (Sesbania spp.), farmyard manure (FYM, 5 t ha−1), azophos containing Azotobacter and phosphate solubilizing bacteria (PSB) @ 15 kg ha−1 and zinc sulphate (ZnSO4) @ 25 kg ha−1 on soil fertility, microbial population i.e. Azotobacter and phosphate solubilizing microorganisms (PSM), N uptake and productivity of kharif rice (variety IET 4786) in gangetic alluvial soils of West Bengal. Rice crop was grown in two successive years (2009 and 2010) during rainy seasons with NPK fertilizers as per state recommendation at varying level in different combination with FYM, GM, biofertilizers, ZnSO4 at recommended dose under irrigated conditions. It is evidenced from the experiment that application of ZnSO4 had a significant positive influence on rice yield as well as on Azotobacter and PSM population when applied in combination with FYM/GM and azophos. The results showed that NP fertilizers at 25% reduced rate compliment 100% NP level in a more or less similar fashion when applied along with 100% K fertilizer, green manuring with dhaincha/FYM, ZnSO4 and azophos for successive years. Maximum grain and straw yield of rice was obtained by application of 100% NPK fertilizer, green manuring with dhaincha, ZnSO4, azophos (4.56 and 5.13 t ha−1 of grain and straw yield, respectively) followed by its 75% NP counterpart (4.47 and 5.02 t ha−1 of grain and straw yield, respectively) and both the treatment effects was found statistically equivalent. Integrated use of green manure at 75% recommended NP dose along with azophos and ZnSO4 enhanced the grain and straw yield by 20.8 and 10.8 per cent, respectively and grain and straw N uptake by 31.7 and 12.4 per cent respectively over 100% NPK alone. Irrespective of treatments, soil health status with respect to soil OC, N, P, K and microbial population has been improved in organic, inorganic and biologically treated combined applications as compared to sole inorganic sources. Application of bio-organic amendment increased plant recovery as well as soil available N in rice crops for subsequent years compared to fertilizer alone. Maximum available N of 226 and 246 kg ha−1 during 1st and 2nd year, respectively was recorded in green manured plot supplemented with ZnSO4, Azotobacter, PSB at 25% reduced level of NP fertilizers.