Tunable cathodoluminescent nanoparticles enable the acquisition of images with both molecular specificity and nanoscale resolution, in a single instrument. Multi-color images can be generated by irradiating nanodiamonds which have been tuned to emit different wavelengths of light upon excitation by an electron beam. Furthermore, these particles can be functionalized, selectively binding to particular structures of interest in the sample. Unlike proteins, these nanoparticles are not damaged under irradiation from the electron beam, and thus they facilitate imaging of biological samples. This technique offers new opportunities for electron microscopy in the physical and life sciences – for instance, from energy storage applications to mapping neural tissues.