Previously isolated strain ATA1 of Enterobacter sp. was used in this work to study various factors affecting degradation of IMI in soil microcosm. Minimal salt medium containing 1% (w/v) glucose was found to be suitable as carbon source for inoculums preparation. Effect of various parameters including soil pH, inoculum size, initial concentration of IMI and flooding of soil for the degradation of imidacloprid in soil were investigated. Strain ATA1 has effectively degraded imidacloprid of range 25−50 mg kg−1 when soil was spiked with different initial concentration of IMI (25−100 mg kg−1) as verified by HPLC analysis. Degradation rate was slower in soil with lower pH compare to neutral pH of soil. An inoculums size of 2 × 107 CFU g−1 of soil was found to be suitable at pH 7 for degrading IMI of 50 mg kg−1. Flooding of IMI spiked soil has also shown significant degradation as compare to nonflooded soil. Metabolites produced after IMI degradation under optimized parameters were identified by GC‐MS analysis. This model study could be used for removal of toxic compounds in field experiments. © 2015 American Institute of Chemical Engineers Environ Prog, 34: 1291–1297, 2015