There has been a rapid increase in the fabrication of various kinds of edible nanoparticles for oral delivery of bioactive agents, such as those constructed from proteins, carbohydrates, lipids, and/or minerals. It is currently difficult to compare the relative advantages and disadvantages of different kinds of nanoparticle-based delivery systems because researchers use different analytical instruments and protocols to characterize them. In this paper, we briefly review the various analytical methods available for characterizing the properties of edible nanoparticles, such as composition, morphology, size, charge, physical state, and stability. This information is then used to propose a number of standardized protocols for characterizing nanoparticle properties, for evaluating their stability to environmental stresses, and for predicting their biological fate. Implementation of these protocols would facilitate comparison of the performance of nanoparticles under standardized conditions, which would facilitate the rational selection of nanoparticle-based delivery systems for different applications in the food, health care, and pharmaceutical industries.