Garlic mustard (Alliaria petiolata) has long been known to degrade mycorrhizal mutualisms in soils it invades and may also promote the abundance of microbial pathogens harmful to native plants or alter saprotrophic communities to disrupt nutrient cycling. Phenology of other invasive species, like Lepidium latifolium and Lonicera maackii, plays a role in their interactions with soil microbial communities, and so we may expect garlic mustard phenology to influence its effects on native soil microbiomes as well. Here, we investigate differences in fungal, bacterial, and archaeal community structure, as well as the abundance of key functional groups, between garlic mustard present, absent, and removed treatments in central-Illinois forest soils across different stages of the garlic mustard life cycle. Across its phenology, garlic mustard present soils had different overall fungal community structure and greater abundance of pathotrophic fungi than soils where garlic mustard was absent or removed. However, abundance of ectomycorrhizal and saprotrophic fungi as well as bacterial and archaeal community structure were similar between treatments and did not interact with garlic mustard phenology. The most abundant overall fungal taxon was a plant pathogen, Entorrhiza aschersoniana, that was greatest in garlic mustard present soils, particularly while the plants were flowering. These results support the hypothesis that invasive plants form active relationships with microbial pathogens that could contribute to their overall success in invading ecosystems.