Abstract Developing edible delivery systems which offer higher protection and release of bioactive constituents is a current challenge in the food industry. The ability of oil-in-water emulsions (20% oil) stabilized by soy or pea protein isolates (4%) to deliver conjugated linoleic acid (CLA, 6%), was studied. The emulsions were prepared by conventional homogenization (550 bar) using one or five homogenization passes. The physicochemical properties of the emulsions were determined, as well as loading capacity and oxidative stability. The emulsions were subjected to in vitro digestion, and tested on absorptive Caco-2 cells. The presence of CLA isomers was followed throughout the process. When comparing similar treatments, soy protein isolate emulsions showed smaller particle size distributions than emulsions prepared with pea protein isolates. Emulsions containing soy proteins showed preferential adsorption of the α’ subunit of conglycinin and the A1, A2, A4 subunits of glycinin on the oil droplets. All emulsions protected the encapsulated CLA better than the non-emulsified control in which CLA was oxidized during storage, as well as after in vitro digestion and delivery in Caco-2 cells. Similar percentages of bioaccessibility and bioavailability of CLA were found for all the emulsion treatments. The results obtained here open new prospects for using oil-in-water emulsions as structured emulsion-based delivery systems to be used in functional foods containing CLA with health enhancing properties.