The intestinal epithelium acts as a key defensive barrier that protects internal organs from the detrimental gut environment. The homeostasis of the gut epithelium may be altered by environmental conditions and exogenous pathogens that can impair the integrity of the gut barrier, leading to immune response associated with low‐grade systemic inflammation, a known contributor to metabolic and inflammatory diseases. Autoimmune diseases (ADs) are a collection of abnormalities of the immune system, in which the immune system of an individual acts against healthy organs or systems, due to a failure in antigenic recognition. Hence, this review aims to focus on modulators of intestinal epithelial barrier dysfunction with effects on autoimmune disorders. All data on dietary phytochemicals and their impact on the modulation of the intestinal epithelium barrier and various ADs were collected from electronic searches of library databases (PubMed, Science Direct, and Google Scholar). An electronic search was conducted using PubMed, Science Direct, and Google Scholar by finding the keywords “phytochemicals” AND “bioactive compounds” AND “flavonoids” AND “polyphenols” OR “intestinal epithelium barrier” OR “autoimmune diseases” OR “inflammatory diseases” in “Title/Abstract/Keywords,” with the date from January 2011 to December 2020, to identify all published studies (in vitro, in vivo, clinical, and case‐control) that have investigated the connection between dietary phytochemicals and their various beneficial effects. Dietary phytochemicals are promising key modulators, stabilizing the integrity of the intestinal barrier and attenuating the progression of ADs. Health‐modulatory information was gathered and orchestrated in a suitable place in this review.