Arthropod communities globally are declining while undergoing taxonomic and functional homogenization, with agricultural activity being a strong contributory factor. Here we use DNA metabarcoding to quantify how variation in climate, agricultural intensity, and plant community composition shape spatiotemporal variation in a metacommunity of > 10,000 arthropod species sampled from 29 Malaise traps across 15 sites in southern Ontario, Canada. Local variation in plant community composition and canopy cover best explained arthropod community dissimilarity. Climatic variables followed closely as explanatory factors, driven primarily by seasonal variation in temperature. The proportion of agricultural land at the landscape scale had no detectable effect. Our results suggest that plant community composition, microclimate, and seasonality structured the arthropod metacommunity to considerable degree, factors that are rarely incorporated into assessments of biodiversity loss due to agriculture. We conclude that habitat restoration on marginal lands is likely an effective strategy for promoting arthropod biodiversity in agroecosystems.