Humans are the result of an evolutionary process, and because of this, many biological processes are interconnected with each other. The intestine–brain axis consists of an intricately connected neuronal–neuroendocrine circuit that regulates the sensation of hunger and satiety. Genetic variations and the consumption of unnatural diets (ultra-processed foods, high contents of sugars, etc.) can override this circuit and cause addiction to certain foods and/or the inability to feel satiety in certain situations. The patients who come to consultations (mainly psychology or nutrition) in an attempt to resolve this problem sometimes fail, which leads to them looking for new strategies based on biological predisposition. This investigation aims to evaluate the genetic studies regarding the microbiota carried out in the last 12 years in humans to try to determine which genes and microbes that have been recently studied are related to patients diagnosed with binge eating disorder or compulsive eating (presenting obesity or not). The protocol followed the PRISMA statement, and the following databases were searched from 2012 until the present day: PubMed, PsycINFO, SCOPUS, and Web of Science. Twenty-four international articles were analyzed, including cross-sectional or exploratory studies; five of them referred to the microbial composition, and in nineteen, the existence of genetic polymorphisms present in binge eating disorder or in compulsive eating could be observed: DRD2, OPRM1, COMT, MC4R, BNDF, FTO, SLC6A3, GHRL, CARTPT, MCHR2, and LRP11. Even though there is still much to investigate on the subject, it must be highlighted that, in the last 4 years, a two-fold increase has been observed in potential markers and in studies related to the matter, also highlighting the importance of different analyses in relation to psychosocial factors and their interaction with the genetic and microbial factors, for which research on the matter must be continued.