The purpose of this work was to study the performance of microspheres of soy protein isolate (SPI), zein, or SPI-zein complex as vehicles of nutraceutical delivery under fasting and prandial conditions in an artificial digestive system (TIM-1). Riboflavin availability for absorption from the small intestine compartments reached 90% of the total load within 4 h, most of it (65-80%) turning up in the jejunum dialysis fluid, suggesting that this segment is the main site of absorption, regardless of the nature of the microspheres. However, the riboflavin concentrations and the availability for absorption profiles depended on microsphere formulation. Release from pure SPI and zein microspheres in the stomach compartment occurred within 15 min. The availability for absorption from both the jejunum and ileum compartment followed first-order kinetics, indicating that the limiting step in nutrient uptake with these two formulations is absorption by passive diffusion. SPI-zein complex microspheres provided sustained release of riboflavin over 4 h and a near-zero-order nutrient availability for absorption profile in both fasting and prandial states. Suspending SPI-zein complex microspheres in yogurt significantly delayed nutrient release, which would increase the likelihood of gastric-sensitive nutrients passing intact into the intestine for absorption. SPI-zein complex microspheres thus show potential for use as nutraceutical delivery vehicles in the creation of novel functional foods.