Identifying the chemical and bonding state of all atoms in a material in three-dimensions remains an unresolved issue. Here, we demonstrate that this information was always intrinsically present within atom probe tomography experimental data, but until now it was overlooked or consciously suppressed. Using an analytical model and robust simulations, we show that the mass peak shape contains information on the ion’s energy loss related to how the atom was bound to the surface, and its neighbourhood. We introduce a complete data processing approach, termed field evaporation energy loss spectroscopy (FEELS), that retrieves and maps variations of the chemical state in 3D with nanometric resolution. We showcase the application of FEELS by analyzing microstructural features and defects in an array of metallic materials. FEELS can be applied on any atom probe data set to more profoundly analyse a material’s characteristics.