Saponins, consisting of sapogenins as their aglycones and carbohydrate chains, are widely found in plants and some marine organisms. Due to the complexity of the structure of saponins, involving different types of sapogenins and sugar moieties, investigation of their absorption and metabolism is limited, which further hinders the explanation of their bioactivities. Large molecular weight and complex structures limit the direct absorption of saponins rendering their low bioavailability. As such, their major modes of action may be due to interaction with the gastrointestinal environment, such as enzymes and nutrients, and interaction with the gut microbiota. Many studies have reported the interaction between saponins and gut microbiota, that is, the effects of saponins on changing the composition of gut microbiota, and gut microbiota playing an indispensable role in the biotransformation of saponins into sapogenins. However, the metabolic routes of saponins by gut microbiota and their mutual interactions are still sparse. Thus, this review summarizes the chemistry, absorption, and metabolic pathways of saponins, as well as their interactions with gut microbiota and impacts on gut health, to better understand how saponins exert their health-promoting functions.