Human travel and global trade have tremendously increased the spread of invasive microorganisms in new regions. Experimental and observational studies in terrestrial ecosystems are beginning to shed light on processes of microbial invasions, their ecological impacts and implications for ecosystem functioning. We provide examples of terrestrial invasive microorganisms, including bacteria, fungi, oomycetes and other protists, and viruses, and discuss the impacts of pathogenic and non-pathogenic invasive microorganisms at levels ranging from host species to ecosystems. This Review highlights that despite the recent progress in microbial invasion research, we are only beginning to understand how alien microorganisms interact with native microorganisms, and the implications of those interactions. Finally, we propose three research themes — microbial interactions, impacts and climate change — to make microbial invasion research a truly integrative discipline.