Abstract Understanding the processes that regulate communities of microorganisms is a key issue and focus in microbial ecology. Although fungi play a critical role in soil biogeochemical cycling, their community assembly processes remain largely unknown, especially in agricultural soils. In this study, we investigated the relative importance of five community assembly processes (variable selection, homogeneous selection, homogeneous dispersal, dispersal limitation and an undominated process) in soil fungal communities under long‐term (28 years, 1990–2018) fertilization management consisting of 12 different treatments in triplicate field plots. Using Illumina MiSeq sequencing of the 18S rRNA eukaryotic gene, we observed that fungal communities in manure treatments were all structured primarily by homogeneous dispersal, whereas the communities in chemical fertilizer treatments were structured primarily by homogeneous dispersal and an undominated process. Soil calcium played an important role in shaping the soil fungal community, whereas soil organic matter concentrations had a considerable impact on the soil fungal phylogenetic community composition. Overall, our results suggest that fertilization management should be considered as a key factor driving microbial community assembly processes in farmed soils. Highlights Soil Ca played a key role in shaping eukaryotic microbial community Chemical fertilization resulted in homogenous selection and undominated processes. A combination of chemical and manure fostered homogenous selection processes.