The human gastrointestinal tract harbours the most complex and abundant community of the human body, the colon being where the highest microbial concentration is found (1012 cell/g). The intestinal microbiota exerts metabolic, trophic and protective functions which are important in the maintenance of the host health. Over recent decades, numerous studies have attempted to provide scientific evidence about the environmental factors that can impact on human health through the modulation of the intestinal microbiota composition. However, this approach is changing, and a new focus on assessing changes at functional level is being developed. If we apply this dual approach to the role played by the diet, it is obvious the need of dynamic gastrointestinal simulation models such as simgi® that allow to evaluate the transformations undergone by food and/or food ingredients during their transit through the gastrointestinal tract, as well as to determine potential changes in the composition and functionality of the intestinal microbiota after food ingestion. So far the studies using the simgi® have confirmed its potential applications in the area of food as a prior step to its application in clinical nutrition to prevent and/or treat diseases associated with intestinal dysbiosis and metabolic disorders. Likewise, this review includes feasible perspectives of the use of simgi® in clinical research concerning to diseases related to the intestinal microbiota.