In this work, the structural features in ZnO:Eu nano-sponges were investigated from micrometre to atomic scale using STEM imaging, spectroscopy, and ePDF, as well as XRD and IR spectroscopy. It was found that at least 10% EuO1.5 could be introduced into the h-ZnO with virtually no change in the structure compared to the 5Eu structure judging from the IR and XRD patterns, while addition of 20% EuO1.5 led to significant formation of an amorphous, 5-10 Å thick Eu-rich inter-crystalline phase, besides the Eu-oxide dispersed as clusters in the ZnO:Eu crystals similar to the 5% EuO1.5 sample studied. The inter-crystalline phase found by HAADF, EDX and EELS mapping, and the latter technique showed that Eu was trivalent in similarity with the Eu(III) in the ZnO:Eu crystals, which is in line with previous studies on 5% Eu samples. The ePDF was applied to get quantitative information on structural deviations on Eu-doping in different samples. The PDF peak intensities provided Eu-O and Eu-Eu distances which for the higher doped 20Eu sample showed peaks at 2.0 Å and 3.2 Å is lower than that of in 5Eu, indicates low possibility to find Zn-O and Zn-Zn atom pair at certain distance. Also, the broadened peak of 20Eu showed the there was more relatively lattice distortion and defects in this sample. The ePDF results are compatible well with all other experimental result above and fit the findings in previous studies. Moreover, the ePDF not only provided information how structure deviated from standard sample, as was acquired from STEM, but also gave precise atom-atom bonding information. The combination of imaging, spectroscopy and ePDF provided a rather unique in-depth spatial understanding of the details of structural variations that arise due to different doping levels. This combination of techniques provide a powerful tool for in-depth materials characterization including crystalline and amorphous phases of complex compositions in sizes down to less than a nanometre, thereby adding information not extractable from standard techniques.