The process of digestion in alligators is a multi-system operation. The alligator has a similar digestive system to that of the crocodile, with minor differences in morphology and enzyme activity.^[1] Alligators have a two-part stomach, with the first smaller portion containing gastroliths. It is believed this portion of the stomach serves a similar function as it does in the gizzard of some species of birds, to aid in digestion. The gastroliths work to grind up the meal as alligators will take large bites or swallow smaller prey whole. This process makes digestion and nutrient absorption easier once the food reaches the second portion of the stomach.^[2] Once an alligators meal has been processed it will move on to the second portion of the stomach which is highly acidic. The acidity of the stomach has been observed to increase once digestion begins. This is due to the increase in CO₂ concentration of the blood, resulting from the right to left shunting of the alligators heart. The right to left shunt of the heart in alligators means the circulatory system will recirculate blood through the body instead of back to the lungs.^[3] The re-circulation of blood leads to higher CO₂ concentration as well as lower oxygen affinity.^[4] There is evidence to suggest that there is increased blood flow diverted to the stomach during digestion to facilitate an increase in CO₂ concentration which aids in increasing gastric acid secretions during digestion.^{[5] [3]} The alligator's metabolism will also increase after a meal by up to four times its basal metabolic rate. ^[6] Alligators also have highly folded mucosa in the lining of the intestines to further aid in the absorption of nutrients. The folds result in greater surface area for the nutrients to be absorbed through. ^[7]

Alligators also have complex microbiomes that are not fully understood yet, but can be attributed to both benefits and costs to the animal. These microorganisms can be found in the high surface area of the mucosa folds of the intestines, as well as throughout the digestive tract. Benefits include better total health and stronger immune system. However alligators are still vulnerable to microbial infections despite the immune boost from other microbiota. ^[7]

During brumation the process of digestion experiences changes due to the fasting most alligators experience during these periods of inactivity. Alligators that go long enough without a meal during brumation will begin a process called autophagy, where the animal begins to consume its fat reserves to maintain its body weight until it can acquire a sufficient meal. ^[8] There is also fluctuation in the level of bacterial taxa populations in the alligator's microbial community between seasons which helps the alligator cope with different rates of feeding and activity. ^[9]