Intensive agricultural activities have caused land degradation due to soil pollution, particularly by pesticides. However, the degradation, metabolism, and toxicity of chiral pesticides by soil microorganisms are often enantioselective. This study aimed to determine the effect of chirality on the degradation of the enantiomers of ethiprole in soil and their impact on soil microbial communities. (R)-ethiprole underwent directional chiral conversion to the (S)-enantiomer in a paddy soil microcosm, leading to elevated concentrations of (S)-ethiprole. Initially, the bacterial operational taxonomic units significantly decreased after 3 days of incubation with rac-ethiprole, (R)-ethiprole, and (S)-ethiprole but gradually increased in the later stage. Principal coordinate analysis revealed that the bacterial community structure was enantioselectively affected by the ethiprole enantiomers. Within 3 days, both rac-ethiprole and (R)-ethiprole reshaped the original stochastic microbial community into a deterministic community (variable selection). Thus, we propose that the enantioselective behavior and ecotoxicology of chiral pesticides need to be considered, especially because there are numerous chiral pesticides currently in use within agricultural management. The comprehensive understanding of the ecological risk of chiral pesticide enantiomers is vital to the process of improving sustainable production and environmental health in agricultural ecosystems.