The spatial correlation between defects in crystalline materials and trace element segregation plays a fundamental role in determining the physical and mechanical properties of a material, which is particularly important in naturally deformed materials. Herein, we combine electron backscatter diffraction, electron channelling contrast imaging, scanning transmission electron microscopy and atom probe tomography on a naturally occurring metal sulphide in an attempt to document mechanisms of element segregation in a brittle-dominated deformation regime. Within APT reconstructions, features with a high point density comprising O-rich discs stacked over As-rich spherules are observed. The combined microscopy data allow us to interpret these as nanoscale fluid inclusions. Our observations are confirmed by simulated APT experiments of core-shell particles with a core exhibiting a very low evaporation field and the shell emulating a segregated layer at the inclusion interface. Our data has significant trans-disciplinary implications to the geosciences, the material sciences, and analytical microscopy.