Increased intake of Western diets and ultra-processed foods is accompanied by increased intake of advanced glycation end products (AGEs). AGEs can be generated exogenously in the thermal processing of food and endogenously in the human body, which associated with various chronic diseases. In food, AGEs can be divided into free and bound forms, which differ in their bioavailability, digestion, absorption, gut microbial interactions and untargeted metabolites. We summarized the measurements and contents of free and bound AGE in foods. Moreover, the ingestion, digestion, absorption, excretion, gut microbiota interactions, and metabolites and metabolic pathways between free and bound AGEs based on animal and human studies were compared. Bound AGEs were predominant in most of the selected foods, while beer and soy sauce were rich in free AGEs. Only 10%–30% of AGEs were absorbed into the systemic circulation when orally administered. The excretion of ingested free and bound AGEs was approximately 90% and 60%, respectively. Dietary free CML has a detrimental effect on gut microbiota composition, while bound AGEs have both detrimental and beneficial impacts. Free and bound dietary AGEs changed amino acid metabolism, energy metabolism and carbohydrate metabolism. And besides, bound dietary AGEs altered vitamin metabolism, and glycerolipid metabolism.