This study investigated the in-vitro digestibility of cold-set whey protein (WP) microgels prepared by two gelation methods (external and internal) containing lipids (0%, 10% or 20% w/w). The incorporation of lipids into these matrices achieved higher entrapment of the bioactive vitamin riboflavin, as well as significant reductions in rates of both the digestion of the protein matrix, and the subsequent diffusion of the water-soluble bioactive. A biexponential model accounted for the contribution of digestion- and diffusion-driven mechanisms in describing the release of riboflavin into enzyme containing simulated gastrointestinal fluids. In particular, for external gelation microgels, as the lipid load within the matrices increased, the contribution of a faster diffusion-driven release was almost completely negated by a slower digestion-assisted release. Lipid loads provided a composite matrix capable of alternating from a burst to a sustained release of bioactive.