The purpose of this study was to examine the effects of biopolymer encapsulation on the digestion of trans fatty acids by using an in vitro human digestion model. We simulated the main components of the human digestive system using a dialysis tubing system that contained synthetic saliva, gastric juice, and digestive enzymes of the small intestine. Trans fatty acid-enriched fat was encapsulated with 1% chitosan, pectin, cellulose, and β-glucan, and passed through the model system. Samples of trans fatty acid-enriched fat that were unencapsulated were more digestible than those that were encapsulated in biopolymers. Moreover, the levels of trans octadecenoic acids (18 : 1t) formed during the digestion of trans fatty acid-enriched fat were decreased upon biopolymer encapsulation. Fat samples enriched with trans fatty acids that were encapsulated with pectin or chitosan had lower free fatty acid contents and lipid oxidation values than unencapsulated control samples. These findings improve our understanding of the effects of biopolymer encapsulation on the digestion of total lipids and trans fatty acids within the gastrointestinal tract.