Increased interannual precipitation variability has deleterious impacts on plant communities in drylands, yet its influence on soil fungal communities is unexplored. In this study, we investigated the effects of long-term increased interannual precipitation variability on soil fungal community dynamics in the Chihuahuan Desert. In a field experiment, we increased precipitation variability using rainout shelters and irrigation to simulate extreme precipitation events. We obtained fungal diversity, community composition, and functional characteristics by sequencing ITS2 amplicons from DNA extracted from soil samples obtained underneath Bouteloua eriopoda (focal grass), Prosopis glandulosa (focal shrub) and bare soil. Soil fungal diversity and community composition differed by host plant identity. We found weak effects of increased precipitation variability on soil fungal diversity and community composition that depended on host plant association and sampling year. Our results suggest that long-term changes in soil fungal communities in response to increased precipitation variability is subtle, and likely mediated by the stronger aboveground plant responses.