The interaction between diet, microbiome, and noncommunicable disease onset is gaining growing attention. The trimethylamine N-oxide (TMAO) is a gut microbiota derivative that has been suggested as a potential regulator of human health, especially (but not exclusively) for its association with cardiovascular diseases. It derives from the trimethylamine (TMA), which is produced by the gut microbiome from dietary precursors, such as choline, betaine, and L-carnitine. Due to the potentially harmful effects of TMAO, strategies aimed to reduce circulating TMAO levels (ranging from dietary restrictions or supplementation to pharmacological treatments) have been proposed. Moreover, TMAO has been suggested as a biomarker of disease onset and prognosis. Nevertheless, contrasting evidence can be found in the literature, and mechanistic explanations or causal demonstrations of the association between the TMA/TMAO metabolism and diseases are still missing. Thus, despite promising findings, the history of TMAO might be more complex than initially hypothesized, and further studies are necessary to promote their translation into clinical practice.