Biological invasions pose a major environmental challenge, often facilitating the unregulated dissemination of pathogens and parasites associated with their hosts. These pathogens can severely impact native and cultivated species, with far-reaching ecological and economic consequences. Despite their importance, the mycobiota associated with invasive plant species remains relatively understudied, posing a complex challenge for researchers. The aim of this manuscript is to underscore the most significant threats posed by the uncontrolled transmission of fungal pathogens from invasive alien plants to native environments and agricultural systems, and to identify the factors influencing this phenomenon. We emphasize the role of pathogen spillback and spillover mechanisms in the domestication of invasive alien plants. The influence of environmental, host, and pathogen-related factors on the survival of fungal pathogens were also investigated. Finally, we explore the technical and legal feasibility of using plant pathogens as “green agents” to control invasive alien plants.