Fat-free yogurt was enriched with vitamin D3 (VD3) loaded into either re-assembled casein micelles (VD3-rCMs) or polysorbate-80 (PS80, or Tween-80) micelles (VD3-PS80). In-vivo VD3 bioavailability was evaluated by a large scale human clinical trial, measuring serum 25(OH)D increases in subjects who consumed fat-free yogurt with 50,000 IU of either VD3-rCM, VD3-PS80, or VD3-free placebo yogurt. VD3-rCM and VD3-PS80 both increased serum 25(OH)D levels by ~8 ng/ml over two weeks, during which no significant differences in mean 25(OH)D levels were observed, evidencing the fact that VD3 bioavailability in rCM is as high as that in the synthetic emulsifier. Rheological measurements following a shear rate sweep showed that VD3-rCM yogurt had a higher apparent viscosity than VD3-PS80 yogurt, and a smaller hysteresis loop. In sensory evaluations, panelists were able to discern between VD3-rCM and VD3-PS80 yogurt, and showed a dislike for PS80 yogurt, compared to rCM or Unenriched control. These results complement our past results showing higher protection against thermal treatment, UV irradiation, and deterioration during shelf life, conferred to hydrophobic nutraceuticals by rCM compared to that by the synthetic surfactant or to the unprotected bioactive, in showing the advantageous use of rCM over the synthetic emulsifier as a delivery system for enrichment of food with VD3 and other hydrophobic nutraceuticals.