The links between deformation-induced microstructures and trace element diffusion is an important theme within material sciences and geosciences. In material sciences, investigating the interplay between impurities and crystalline defects has had a significant impact on improving the design of synthetic materials [1, 2]. As for geochronology, the reliable use of minerals such as zircon and titanite as U-Th-Pb geochronometers requires minimal radiogenic isotope and trace element mobility [3, 4]. Deformationinduced redistribution of trace elements within minerals can affect isotopic ratios, significantly impacting the reliability of geochronometers. In economic geology, the incorporation of base-and precious-metals in sulphide minerals has significant implications for metallic ore paragenesis [5]. It has recently been illustrated that plastic deformation in pyrite creates diffusion pathways as subgrain boundaries that act as traps for base-and precious-metals [6]. However, the plastic behaviour of pyrite and the diffusion mechanisms driving trace elements in microstructures remain poorly understood. In this study, we attempt to document the diffusion processes driving trace elements into deformation-induced microstructures of sulphides by developing new applications to 2D and 3D nanostructural and geochemical imaging techniques. Herein, we integrate electron backscatter diffraction (EBSD) mapping, electron channeling contrast imaging (ECCI) and atom probe tomography (APT) on crystal-plastically deformed pyrite. Our study pushes the limits of the 3D tools' abilities by applying new data processing techniques that allow crystallographic-orientation measurement of nanostructural crystal defects.