The intestinal barrier plays a central role in sustaining gut homeostasis and, when dysfunctional, may contribute to diseases. Dietary flavonoids derived from Citrus genus represent one of the main naturally occurring phytochemicals with multiple potential benefits for the intestinal barrier function. In the intestine, citrus flavonoids (CFs) undergo ingestion from the lumen, biotransformation in the epithelial cells and/or crosstalk with luminal microbiota to afford various metabolites that may in turn exert protective actions on gut barrier along with their parental compounds. Specifically, the health‐promoting properties of CFs and their metabolic bioactives for the intestinal barrier include their capacity to (a) modulate barrier permeability; (b) protect mucus layer; (c) regulate intestinal immune system; (d) fight against oxidative stress; and (e) positively shape microbiome and metabolome. Notably, local effects of CFs can also generate systemic benefits, for instance, improvement of gut microbial dysbiosis helpful to orchestrate gut homeostasis and leading to alleviation of systemic dysmetabolism. Given the important role of the intestinal barrier in overall health, further understanding of underlying action mechanisms and ultimate health effects of CFs as well as their metabolites on the intestine is of great significance to future application of citrus plants and their bioactives as dietary supplements and/or functional ingredients in medical foods.