Microorganisms are ubiquitous in soil, air, and water ecosystems, where they are key players of ecosystem services. Microbial ecotoxicology is an emerging interdisciplinary area of research which aims at investigating the impact of human activities on the diversity, abundance, and activity of microorganisms. In return, the results of such investigations hold the promise to provide novel ways of assessing in a sensitive way the impacts of diverse environmental disturbances and subsequent ecosystem responses. Thus and although the term itself is yet rarely encountered in the scientific literature, microbial ecotoxicology already addresses an increasing political and societal demand. In the French scientific landscape, which often mimics the famous (but sometimes indigestible) “mille-feuilles” pastry, microbial ecotoxicologists are scattered across many different research centers belonging to different research organizations and universities. This research field has thus lacked any visibility and remained unorganized until now. Formal organization of scientific activities may be considered a typical “froggies” concern (or ailment). Nevertheless, it is rather surprising that scientific journals and significant international conferences specifically devoted to microbial ecotoxicology have been missing so far, especially considering the plethoric range of journals and congresses devoted to microbial ecology and ecotoxicology. With these considerations in mind, the idea of organizing the French research community of microbial ecologists around concepts of ecotoxicology made its way, with the aim of sharing the necessity to overcome artificial boundaries that prevent progress in this promising field.