Fertilizer and fungicide applications are commonly used in lowbush blueberry cropping systems (Vaccinium angustifolium Aiton and Vaccinium myrtilloides Michaux) to enhance fruit yield. Such crop inputs can significantly affect soil fungi, a topic that is not well documented, even though these organisms impact the development and survival of lowbush blueberries in natural forest ecosystems. We evaluated soil fungal biomass and community structure in a commercial lowbush blueberry field located in Lac-Saint-Jean, Québec, Canada. Since 2017, mineral fertilizers and fungicide (Proline 480 SC®) have been applied once every 2 years. In-growth sandbags were incubated for 90 days during the 2019 and 2020 growing seasons to collect fungal hyphae biomass in vegetated and unvegetated areas. Soil samples were also collected to analyze the structure of the fungal community using next-generation sequencing. Our results showed that applying fungicide alone increased hyphal biomass in sandbags by 40%, whereas adding both fungicide and fertilizer or fertilizer alone did not change hyphal biomass compared to the control. The structure of the fungal community was only slightly affected by the applications of fungicide and fertilizer, with fungicide decreasing the relative abundances of plant pathogens and fertilizer negatively influencing saprotrophs. Low doses and infrequent applications could explain such weak effects. Among the 33 amplicon sequence variants that were positively associated with the presence of lowbush blueberry plants, eight Penicillium species, four Clavariaceae, two Serendipita species, and one ericoid mycorrhizal fungi (Oidiodendron maius) were identified.