Zinc oxide (ZnO) is a semiconductor with a wide range of applications, and often the properties are modified by metal-ion doping. The distribution of dopant atoms within the ZnO crystal strongly affects the optical and magnetic properties, making it crucial to comprehend the structure down to the atomic level. Our study reveals the dopant structure and its contents in Eu-doped ZnO nanosponges with up to 20% Eu-O clusters. Eu was distributed over the ZnO:Eu crystals, with an additional amorphous intercrystalline phase observed, especially in the 20% Eu sample. The electron pair distribution function revealed the presence of nonperiodic Eu3+-oxide clusters and proved highly effective for analyzing the coordination environment of Eu-O, ranging from 2.0 to 2.8 & Aring;. It uncovered three-, four-, and five-coordinate Eu-O configurations in the 20% Eu sample, and there were significant changes in Eu coordination between the samples, which is ascribed due to the intercrystalline phase. The proposed method offers a potential characterization routine for a detailed investigation of complex doped materials.