During the past 12000 years agricultural systems have transitioned from natural habitats to conventional agricultural regions and recently to large areas of genetically engineered (GE) croplands. This GE revolution occurred for cotton in a span of slightly more than a decade during which a switch occurred in major cotton production areas from growing 100% conventional cotton to an environment in which 95% transgenics are grown. Ecological interactions between GE targeted insects and other insectivorous insects have been investigated. However, the relationships between ecological functions (such as herbivory and ecosystem transport) and agronomic benefits of avian or mammalian insectivores in the transgenic environment generally remain unclear, although the importance of some agricultural pest management services provided by insectivorous species such as the Brazilian free-tailed bat, Tadarida brasiliensis, have been recognized. We developed a dynamic model to predict regional-scale ecological functions in agricultural food webs by using the indicators of insect pest herbivory measured by cotton boll damage and insect emigration from cotton. In the south-central Texas Winter Garden agricultural region we find that the process of insectivory by bats has a considerable impact on both the ecology and valuation of harvest in Bacillus thuringiensis (Bt) transgenic and nontransgenic cotton crops. Predation on agricultural pests by insectivorous bats may enhance the economic value of agricultural systems by reducing the frequency of required spraying and delaying the ultimate need for new pesticides. In the Winter Garden region, the presence of large numbers of insectivorous bats yields a regional summer dispersion of adult pest insects from Bt cotton that is considerably reduced from the moth emigration when bats are absent in either transgenic or non-transgenic crops. This regional decrease of pest numbers impacts insect herbivory on a transcontinental scale. With a few exceptions, we find that the agronomics of both Bt and conventional cotton production is more profitable when large numbers of insectivorous bats are present.