Non-target effects of deliberately released organisms into a new environment are of great concern due to their potential impact on the biodiversity and functioning of ecosystems. Whereas these studies often focus on invasive species of macro-organisms, the use of microbial inoculants is often expected to have specific effects on particular functions but negligible overall effects on resident microbial communities. Here, we posit that such introductions often impact native microbial communities, which might influence ecosystem processes. Focusing on soil communities, we used a literature search to examine the impact of microbial inoculation (often the release of beneficial microorganisms in agricultural systems) on resident microbial communities. Of 108 studies analyzed, 86% showed that inoculants modify soil microbial communities in the short or long term. In addition, for studies analyzing the consequences of microbial inoculants in the longer term, 80% did not observe the resilience (return to the initial state) of the resident community following inoculation. Through the knowledge gathered from each study, we propose a synthetic and mechanistic framework explaining how inoculants may alter resident microbial communities. We also identify challenges as well as future approaches to shed more light on this unseen reality.