Pesticide seed treatments (PST) which contain fungicides and insecticides are commonly used in agriculture; however, little is known about their effect on soil microbial communities and soil health. Neonicotinoids – controversial insecticides which are common in PST – have received criticism due to potential non-target effects. While fungal pathogens need to be moderated, PST have the potential to disturb broader fungal communities which could lead to reduced nutrient cycling and poor soil health. Given the broad use of PST, their effect on soil fungi needs to be studied within the context of other agricultural management practices. For example, tillage regimes can result in distinct fungal communities which may respond differently to PST. An experimental site was established in 2013 with a corn-soy rotation under three tillage treatments: Full-till, Strip-till, and No-till. Since 2016, seeds with or without PST (fungicides and insecticides) were planted under each tillage regime in a fully factorial design. In 2018, bulk soil was collected from within rows while soy was growing. A range of soil physicochemical variables were measured, and soil function was determined with substrate-induced respiration and enzyme assays. DNA was extracted from soil and the ITS region was sequenced to determine fungal community structure and diversity. While tillage significantly affected fungal community structure (p < 0.01), there was no effect of PST on either community structure (p = 0.59) or diversity (p = 0.52). This indicates that PST does not affect bulk soil fungal communities; however, they may have an impact at different temporal or spatial scales than those studied here. Across all treatments, fungal community structure correlated with soil water holding capacity (rs = 0.23, p = 0.04) and electrical conductivity (rs = 0.26, p = 0.01). Despite not finding an effect of PST on fungal communities, we did find that PST increased potentially mineralizable nitrogen under no-till and shifted community level physiological profiles determined by substrate-induced respiration. These results suggest that while PST can affect certain aspects of soil health, there are no clear effects on the soil fungal community.