Trace elements diffuse negligible distances through the pristine crystal lattice in minerals: this is a fundamental assumption when using them to decipher geological processes. For example, the reliable use of the mineral zircon (ZrSiO4) as a U-Th-Pb geochronometer and trace element monitor requires minimal radiogenic isotope and trace element mobility. Here, using atom probe tomography, we document the effects of crystal-plastic deformation on atomic-scale elemental distributions in zircon revealing sub-micrometre-scale mechanisms of trace element mobility. Dislocations that move through the lattice accumulate U and other trace elements. Pipe diffusion along dislocation arrays connected to a chemical or structural sink results in continuous removal of selected elements (for example, Pb), even after deformation has ceased. However, in disconnected dislocations, trace elements remain locked. Our findings have important implications for the use of zircon as a geochronometer, and highlight the importance of deformation on trace element redistribution in minerals and engineering materials.