Ni contamination from crude oil in the fluid catalytic cracking (FCC) process is one of the primary sources of catalyst deactivation, thereby promoting dehydrogenation–hydrogenation and speeding up coke growth. Herein, single‐particle X‐ray fluorescence, diffraction and absorption (μXRF‐μXRD‐μXAS) tomography is used in combination with confocal fluorescence microscopy (CFM) after thiophene staining to spatially resolve Ni interaction with catalyst components and study zeolite degradation, including the processes of dealumination and Brønsted acid sites distribution changes. The comparison between a Ni‐lean particle, exposed to hydrotreated feedstock, and a Ni‐rich one, exposed to non‐hydrotreated feedstock, reveals a preferential interaction of Ni, found in co‐localization with Fe, with the γ‐Al2O3 matrix, leading to the formation of spinel‐type hotspots. Although both particles show similar surface zeolite degradation, the Ni‐rich particle displays higher dealumination and a clear Brønsted acidity drop.