Context Invasive plants are one of the most significant threats to woodlands globally. Methods of invasive plant control include manual removal and herbicide application. While the impacts of control methods on invasive and off-target native plant species are often explored, the impacts on below-ground organisms, such as fungi, are less well understood.Aims We conducted a glasshouse trial to investigate the responses of soil fungal communities to herbicides and manual removal that are used to control common invasive plant species in Banksia woodland in south-western Australia.Methods Broad spectrum (glyphosate and pelargonic acid) and grass-specific (fluazifop-p-butyl) herbicides were separately applied to pots containing either Ehrharta calycina, a key invasive grass species or Eucalyptus todtiana, a native woodland tree at the recommended woodland rate. After six weeks, samples of treated soils were subjected to high throughput sequencing to determine fungal community diversity, richness, relative abundance, composition and putative ecosystem function.Key results Pelargonic acid induced the widest range of changes including decreased fungal richness and Shannon diversity but all herbicides affected community composition. Within functional groups, fluazifop-p-butyl led to a significant decrease of symbiotrophs in the mycorrhizal species.Conclusions We show that invasive species management, in the manner applied, can lead to immediate changes in fungal community composition.Implications Observed patterns require further exploration, particularly repeat testing under different environmental conditions, to better determine the impact and mode of action of herbicides on below-ground organisms. The functional changes in the soil fungal community could further disturb the soil fungal community and complicate subsequent management considerations.