This report describes the work developed during the execution of the Review Impact MICrobiome In Assesment (RIMICIA) project. This project has performed a comprehensive and critical assessment of the evidence‐based research about: i) the impact of dietary compounds in the human and some domestic animals (i.e., poultry, ruminants and pigs) gut microbiome; ii) the most representative in vitro and in vivo models of the human gut microbiota currently used in microbiome research studies; and iii) the methodology used to measure changes in the microbiota. This project has also gathered and appraised information about the exposure to a series of dietary xenobiotics that may cause oxidative damage and inflammation in the gut, as well as on how this exposure may affect the host gastrointestinal tract architecture and/or organisation, such as disruption of the intestinal barrier, enhancement of bacteria and bacteria products translocation into the circulation, and immune cell toxicity in humans and domestic animals. However, research studies are generally scarce on the structure‐function relationship, the underlying mechanisms of the host‐microbiome interactions and dose‐dependent effects. Based on this information, a roadmap is proposed encompassing a prioritisation strategy targeting dietary compounds with potential for disrupting the gut microbiome composition which are increasingly present in modern and westernised diets (e.g., additives, chemical contaminants) and an explanation as to why the safety assessment of these compounds could benefit from gut microbiome data integration in the future. A multidisciplinary research strategy is proposed to provide key information to fill knowledge and methodology gaps. At a later stage, this research strategy could also provide useful information for developing policy actions aiming at the elaboration of decision frameworks for the future incorporation of gut microbiome data into specific guidelines in Organisation for Economic Co‐operation and Development (OECD) or other international test guidelines and, ultimately, into regulatory programs.