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The Brazilian pepper tree (Schinus terebinthifolius) is an invasive species that requires significant disturbance to eradicate. Previous studies have identified associations between the Brazilian pepper tree and ectomycorrhizal fungi (EMF). However, limited research has explored the connection between disturbance from removal and the effect on EMF. This study investigated the sensitivity of EMF and the broader fungal community to the full and selective removal of the Brazilian pepper tree. During the selective removal of Brazilian pepper tree, we examined the mycorrhizal community of the Arroyo willow (Salix lasiolepis) to assess the influence of the restoration disturbance on native species. We used ITS2 sequencing to identify the EMF present during the restoration. Our expectation was that both removal efforts would reduce the presence of EMF. Contrary to our predictions, full removal increased EMF richness and relative abundance in the soil. As anticipated, selective removal reduced the richness and relative abundance of EMF associated with soil. Selective removal led to a decrease in the richness of EMF in arroyo willow roots with no effect on relative abundance. Moreover, fungal community composition in soil and roots shifted significantly during selective and full removal. However, the community composition of EMF, specifically, remained constant across treatment types. During full removal efforts, the application of organic soil amendments may have contributed to the increase in the diversity and relative abundance of EMF. Selective removal will require additional measures, such as soil amendments, to curtail the loss of EMF.