Treatment of malabsorption should focus on the underlying cause as well as correcting any existing nutritional deficiencies. Treatment options and prevention methods for patients with malabsorption may differ, based on the type, cause and severity of the condition.

Treatment of malabsorption due to food intolerances may involve simply avoiding those foods a patient is unable to digest. For patients with lactose intolerance, this means avoiding dairy products that contain lactose. Patients with celiac disease should avoid gluten (a protein found in wheat, rye, oats and barley), due to an inability to absorb it. 

Medications may also be used to treat some causes of malabsorption. For example, antibiotics may be used to treat malabsorption caused by infection or bacterial overgrowth in the small intestine. Anti-inflammatory medication may be used to treat patients with malabsorption as a result of Crohn's disease.

Replacing or supplementing nutrients lost during malabsorption may also be necessary. This can include taking supplements or choosing dietary alternatives to replace lost fats, carbohydrates, proteins, vitamins and minerals. For example, a parenteral formula containing medium-chain triglycerides (fats with an unusual chemical structure the body can easily digest) have been used as a fat substitute. In addition, patients with pancreatic insufficiency may wish to take specific supplements (protease and lipase) to make up for the digestive enzymes their pancreas is unable to produce.

In severe cases of malabsorption, intravenous feeding (total parenteral nutrition) may be required. This may be recommended after bowel resection surgery or to avoid aggravating inflamed or damaged intestines.