A long-term experiment was commenced (2011) and conducted at the Research Farm of Dapoli (Maharashtra) during Kharif and Rabi season in rice–groundnut cropping system, to evaluate the effect of green manuring and different weed control measures on the survival and growth of total bacteria, total fungi, total free living nitrogen fixers and total phosphate solubilizers in rhizospheric soil. Results emerged out from the conduct during 2011 to 2014 indicated that, green manuring (in-situ application of Sesbania rostrata 45 DAS) and without green manuring (control) as a main plot treatment and among the weed control measures and sub plot treatments comprising, comparative effects of hand weeding, fixed herbicide pretilachlor (pre-emergence) for rice crop and pendimethalin (pre-emergence) for groundnut crop, and different rotational herbicides (for rice crop, pyrazosulfuron 0.030 kg/ha at 8-10 DAT (1 year), fenoxaprop -p-ethyl 0.056 kg/ha at 25-30 DAT (2 year), oxadiargyl 0.100 kg/ha at 0-5 DAT (3 year), and for groundnut crop oxadiargyl 0.12 kg/ha at 0-2 DAS-1 year, butachlor 1.0 kg/ha at 0-3 DAS-2 year, alachlor1.5 kg/ha at 0-3 DAS-3 year) application to both the crops were significantly tested along with weedy check. The results concluded that the green manuring significantly increased in microbial populations than without green manuring. There were no adverse effects of herbicidal use on all the estimated microbial population at all the stages of both the crops. In contrast to use of fixed herbicide pretilachlor-S 0.75 kg/ha for rice and pendimethalin 1.00 kg/ha and different rotational herbicides had no long-term adverse effects on rhizosphere micro-flora of rice–groundnut cropping system.