Digestive enzymes, such as proteases and lipases, are widely recognized for their crucial roles in the ripening and production of fermented foods. Digestive enzymes are also used as supplements in nonruminant livestock to enhance feed digestion and promote animal growth. However, information on the effects of exogenous digestive enzymes on gut health and disease remains limited. Notably, recent studies show that consuming proteases and lipases can increase the levels of beneficial bacteria and short-chain fatty acids in rodent gut. These findings led us to hypothesize that intestinal proteases and lipases play beneficial roles by enriching beneficial bacteria. To examine this hypothesis, we reviewed recent studies on the potential effects of exogenous digestive enzymes on gut microbiota composition and overall health. Consistent with the hypothesis, all 13 studies in this review reported significant improvements in animal gut microbiota composition with the dietary supplementation of proteases and lipases. Additionally, the possible mechanisms of the prebiotic-like effects of the enzymes through increased nutrient digestion were discussed. This review explores how exogenous proteases and lipases influence gut microbiota composition and overall health. This is the first review to provide insights into the potential roles of exogenous digestive enzymes as prebiotics.