The study describes the effect of saponins, isolated from a medicinal plant Azadirachta indica on the CNS enzymes of a stored grain pest, Tribolium castaneum and a socioeconomic insect, Apis mellifera. A comparative study was designed to identify the role of saponins on insect acetylcholinesterase (AChEs). The enzyme activities were tested for the effect of saponins. The AChE activity of T. castaneum was inhibited by the saponins and follows competitive inhibition kinetics. In case of A. mellifera enzyme activity was not inhibited. In vitro and in vivo inhibition was observed for T. castaneum at larval stages, in dose dependent and time dependent manner. LC50 was determined to be 0.7ppm. To investigate the different effects of saponins on A. mellifera and T. castaneum AChE, computational approach was employed. For this purpose a dissection of 3-D model of A. mellifera and T. castaneum AChE enzyme was studied which showed that change in amino acid sequence of primary structure of enzyme exists at the saponin binding site, resulting in weak interaction for A. mellifera as compared to T. castaneum enzyme protein. Computational studies inidicate that A. mellifera enzyme had a little binding affinity for saponin as compared to T. castaneum AChE. The amino acid residues of T. castaneum AChE identified at positions 259(SER), 176(SER), 173(GLY), and 502 (HIS) are involved in binding with saponin molecule to form four hydrogen bonds. Whereas in A. mellifera hydrogen bonds are formed at two positions by SER 171 and TYR104 with the saponin molecule indicating weak interaction as compared to T. castaneum Saponins derived from A. indica work as biosafe pesticides as it has no considerable effect on CNS enzymes of A. mellifera (a major plant pollinator and friendly insect) as compared to T. castaneum.