Changing pesticide use is frequently implicated as a driver of declines in butterfly abundance. Existing empirical evidence of linkages between pesticide use and butterfly abundance is limited to studies that fail to account for the full suite of pesticides used by farmers, which fail to account for the effects of substitute pesticides. In this paper, we bring together data on the use of the six principal pesticide groups on corn and soybean fields and butterfly abundance data to create a unique county-level panel dataset spanning the 60 counties in the American Midwest over 17 years. We estimate count data models of total butterfly abundance, the abundance of 16 species, and distinct species identified to measure the effects of each pesticide group while controlling for climate and land use confounders. We find that neonicotinoids, a group of systemic insecticides applied to corn and soybean seeds before planting, have a strong negative association with butterfly diversity and two of our four indicator species, including Monarch butterflies. Further, we find a positive association between the planting Bacillus thuringiensis (Bt) traited corn seeds and butterfly abundance, though only in counties with large areas of cropland where interaction between butterflies and affected cropland is likely. We estimate that farmers’ changes in pesticide use since 1998 has accounted for a 9% decrease in overall butterfly abundance in the median county in our sample, driven by a shift towards neonicotinoid seed treatments since the mid-2000s.