In this work, we take on an in-depth characterization of the complex particle structures made by spray flame synthesis. Because of the resulting hierarchical aggregates, very few measurement techniques are available to analyze their primary particle and fractal properties. Therefore, we use small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) to investigate the influence of the precursor concentration on the fractal structures of zirconia nanoparticles. The combination of information gained from these measurement results leads to a detailed description of the particle system, including the polydispersity and size distribution of the primary particles. Based on our findings, unstable process conditions could be identified at low precursor concentrations resulting in the broadest size distribution of primary particles with rough surfaces. Higher precursor concentrations lead to reproducible primary particle sizes almost independent of the initial precursor concentration. Regarding the fractal properties, the typical shape of aggregates for aerosols is present for the investigated range of precursor concentrations. In conclusion, the consistent results for SAXS and TEM show a conclusive characterization of a complex particle system, allowing for the identification of the underlying particle formation mechanism.