Mounting evidence points to a global collapse in insect populations, with some of the best documented evidence among butterfly species. While habitat loss, climate change, and agricultural pesticides have all been implicated, researchers have pointed to glyphosate herbicides and neonicotinoid insecticides specifically as potential causes of insect declines. But the focus on individual pesticides or individual insect species or groups fails to grapple with the complex dynamics of how agricultural practices vary and correlate through time and space. By examining a comprehensive set of insecticide and herbicide classes from thousands of farm records over the years 1998-2014 and linking them with systematic butterfly abundance surveys across 60 Midwestern U.S. counties, this research disentangles correlated pesticide effects across butterfly species. For the median county in our sample, we find an 8% decline in total butterfly abundance due to changing pest control systems, with declines pronounced among forb-hosted specialist species including monarchs, for which populations declined 33.5% relative to predictions under historic pest control technologies. Neonicotinoid-treated seeds bear primary responsibility, while there appears to be no consistent negative effect from crop seed that incorporate Bacillus thuringiensis (Bt) proteins nor from glyphosate herbicide. Better public data are needed on pesticides applied to crop seed in order inform policy about environmental safety.