Organic aerosols are key components of the Earth's atmospheric system. The phase state of organic aerosols is known to be a significant factor in determining aerosol reactivity, water uptake and atmospheric lifetime – with wide implications for cloud formation, climate, air quality and human health. Unsaturated fatty acids contribute to urban cooking emissions and sea spray aerosols. These compounds, exemplified by oleic acid and its sodium salt, are surface-active and have been shown to self-assemble into a variety of liquid-crystalline phases upon addition of water. Here we observe a crystalline acid–soap complex in acoustically levitated oleic acid–sodium oleate particles. We developed a synchrotron-based simultaneous small-angle and wide-angle X-ray scattering (SAXS and WAXS)–Raman microscopy system to probe physical and chemical changes in the proxy during exposure to humidity and the atmospheric oxidant ozone. We present a spatially resolved structural picture of a levitated particle during humidification, revealing a phase gradient consisting of a disordered liquid crystalline shell and crystalline core. Ozonolysis is significantly slower in the crystalline phase compared with the liquid phase, and a significant portion (34 ± 8 %) of unreacted material remains after extensive oxidation. We present experimental evidence of inert surface layer formation during ozonolysis, taking advantage of spatially resolved simultaneous SAXS–WAXS experiments. These observations suggest that atmospheric lifetimes of surface-active organic species in aerosols are highly phase-dependent, potentially impacting climate, urban air quality and long-range transport of pollutants such as polycyclic aromatic hydrocarbons (PAHs).