Numerous anthropogenic chemicals of environmental concern--including some phenoxy acid herbicides, organophosphorus insecticides, polychlorinated biphenyls, phthalates, freon substitutes and some DDT derivatives--are chiral. Their potential biological effects, such as toxicity, mutagenicity, carcinogenicity, and endocrine disrupter activity, are generally enantiomer-selective, and different enantiomers are preferentially degraded (transformed) by micro-organisms in various environments. Here we use field and laboratory experiments to demonstrate that environmental changes in soils can alter these preferences, and to suggest that the preferences shift owing to different groups of related microbial genotypes being activated by different environmental changes. In Brazilian soils, almost all pasture samples preferentially transformed the non-herbicidal enantiomer of dichlorprop ((RS)-2-(2,4-dichlorophenoxy)propionic acid), while most forest samples either transformed the herbicidal enantiomer more readily or as rapidly as the non-herbicidal enantiomer. Organic nutrient enrichments shifted enantioselectivity for methyl dichlorprop ((RS)-methyl 2-(2,4-dichlorophenoxy)propionic acid) strongly towards preferentially removing the non-herbicidal enantiomer in soils from Brazil and North America, potentially increasing phytotoxicity of its residues relative to that of the racemate. Assessments of the risks chemical pollutants pose to public health and the environment need to take into account the chiral selectivity of microbial transformation processes and their alteration by environmental changes, especially for pesticides as up to 25 per cent are chiral.