Nanoparticulate systems intended for the use in drug delivery are getting more and more complex. Composite nanoparticles, such as core-shell particles are designed in order to be used for co-delivery of drugs or a modified release profile. Often the structure can only be postulated by the preparation process, such as surface polymerization, but cannot be experimentally determined due to a lack of appropriate analytical methods. Here a core-shell particle system composed of two biodegradable and biocompatible materials, gelatin and PLGA, is developed. In order to reveal the actual polymer distribution, a combination of cryo-transmission electron microscopy and energy-filtered transmission electron microscopy was established. Using the occurrence of specific elements in combination with degradation kinetics induced by the electron beam allows to conclude on the nanoparticles’ architecture. Based on these methods and thus, the particle composition, the drug delivery system can be further developed.