Cistus ladanifer scrublands are widely distributed in the Mediterranean basin and represent an early stage of secondary succession following major disturbances (e.g., fire). This vegetation type often establishes on disturbed and poor soils, thereby improving soil stability in stress-prone environments. Fire prevention treatments in these scrublands are often recommended to decrease the risk of wildfires, but the effect of these treatments on associated soil fungi is not known. We studied the effect of distinct fire prevention treatments on soil fungal communities associated with C. ladanifer scrublands soils. We used Illumina MiSeq sequencing of the ITS1 region on soil samples taken after distinct fire prevention treatments that were performed in 27 plots belonging to a long-term experiment. Recent fire prevention treatments did not affect overall fungal community composition nor fungal diversity; however, when analyzing the community according to the functional guilds, the relative abundance of ectomycorrhizal species was significantly lower in burned and 100% cleared plots, compared with control and 50% cleared plots. In contrast, site history affected fungal community composition and richness to a greater extent than the fire prevention treatments. Our results show a higher susceptibility of ectomycorrhizal species to recent high-intensity fire prevention treatments, whereas fire prevention treatments of medium intensity may reduce the risk of wildfire and maintain the soil fungal community.