This dataset contains experimental results obtained during the development of a microfluidic system designed to produce and evaluate high internal phase emulsions (HIPEs). The data include the formulation, stability, and digestion behavior of W/O HIPEs generated within microchannels simulating the small intestine environment. Comparisons were made between the microfluidic digestion outcomes and those obtained using the standardized INFOGEST in vitro digestion protocol, supporting the validation of the intestinal microsystem developed in this work. The data cannot be made available due to intellectual property protection. For more information, please contact the corresponding authors.