Insecticide and fungicide seed treatments are commonly used to control pests and pathogens in conventional maize and soybean culture, but little is known about their effects on the communities of non-target microbes that inhabit the rhizospheres or leaves of these crops. Because rhizosphere bacterial and fungal communities influence carbon and nutrient turnover, nutrient transformation, nutrient uptake and disease suppression, and because leaf endophyte fungal communities influence many aspects of stress tolerance in plants, any effect of a pesticide seed treatment on these microbial communities could have unintended and possibly adverse effects on seedling performance. We conducted a three-year field experiment in which maize (2013, 2015) and soybean (2014) were grown in rotation from seeds that were either coated or not coated with common pesticide treatments, which included contact and systemic fungicides and systemic insecticides. We sampled seedling rhizosphere soil (maize in 2013, soybean in 2014) and seedling leaves (soybean in 2014, maize in 2015) and characterized their microbial communities. For maize, the rhizosphere fungal and bacterial communities were significantly affected by the seed treatment, but leaf endophytic fungal communities were not. For soybean, the rhizosphere fungal community was significantly affected, as was the leaf endophytic fungal community, but not the rhizosphere bacterial community. These results show that pesticide seed treatments may affect rhizosphere soil microbial communities and endophytic leaf fungal communities more than one month after planting and, therefore, may have significant, unintended effects on non-target organisms. Additional research must determine the consequences of these effects and the nature of their context dependency.