Non-caloric artificial sweeteners (NAS) are common food supplements consumed by millions worldwide as means of combating weight gain and diabetes, by retaining sweet taste without increasing caloric intake. While they are considered safe, there is increasing controversy regarding their potential ability to promote metabolic derangements in some humans. We recently demonstrated that NAS consumption could induce glucose intolerance in mice and distinct human subsets, by functionally altering the gut microbiome. In this commentary, we discuss these findings in the context of previous and recent works demonstrating the effects of NAS on host health and the microbiome, and the challenges and open questions that need to be addressed in understanding the effects of NAS consumption on human health.