The in vitro digestion of a self nano-emulsifying drug delivery system (SNEDDS) was visualized by cryogenic transmission electron microscopy (Cryo-TEM). The dynamic lipolysis model, simulating the environment of the gastrointestinal tract in fasted conditions, was used for this purpose. The results revealed that micelles are present during the entire lipolysis process. Oil droplets from the self nano-emulsifying drug delivery system are transformed to spherical or elongated unilamellar vesicles as lipolysis progresses. Low numbers of bilamellar and open vesicles were detected. After 50% hydrolysis a decrease in the number of unilamellar vesicles and oil droplets was observed. Furthermore, the electrical properties of the oil droplets were investigated by measuring their zeta-potential values as a function of time. An increase (in absolute values) to the zeta-potential of the hydrolyzing SNEDDS droplets observed versus time implying (binding or incorporation) of the micelles to the surface. The current data emphasize that Cryo-TEM combined with the in vitro dynamic lipolysis model can offer useful information on the formation of the various colloid phases during in vitro digestion of lipid-based formulations. Furthermore, it can provide a better understanding of the in vivo behavior of these systems, as well the solubilization of lipophilic drug compounds, offering new insights for designing and optimizing oral lipid-based formulations and possibly predicting their in vivo behavior. Such methodology can be a useful tool for the strategic development of lipid-based formulations.