Microencapsulation provides a vehicle for the incorporation of fats and oils into powders that can be used as dry ingredients in an expanded variety of food products. Microencapsulated omega-3 oils in particular are commonly incorporated into a variety of foods and numerous in vitro studies have examined the impact of individual microencapsulation technologies on the simulated digestibility of the oil core. We have exposed twelve microencapsulated canola oil-in-water emulsions, formulated with different proteins (milk or soy) or mixtures of protein and carbohydrates (sugars, oligosaccharides, resistant starch) and processed into powders by spray drying, to simulated gastric and intestinal fluids in vitro. The extent of lipolysis of the canola oil in these products varied between 12–68% suggesting that the in vitro digestibility of the oil within the powders was dependent on both the formulation and the processing steps used in their manufacture. Five microencapsulated powders with differing extents of in vitro lipolysis were then incorporated into a dairy beverage for an in vivo human trial with neat oil incorporation in the beverage used as the control. Measurement of triglyceride levels in blood revealed both enhanced peak height and area under the curve (AUC) in vivo for the microencapsulated oil groups when compared to the neat oil control. The range of lipolysis efficiencies observed with the different formulations in vitro was not reflected in vivo. These observations suggest that care needs to be taken when extrapolating data from in vitro lipolysis to bioavailability in humans.