Negatively charged nitrogen-vacancy (NV−) centers in diamond have generated much recent interest for their use in sensing. The sensitivity improves when the NV ground-state microwave transitions are narrow, but these transitions suffer from inhomogeneous broadening, especially in high-density NV ensembles. To better understand and remove the sources of broadening, we demonstrate room-temperature spectral “hole burning” of the NV ground-state transitions. We find that hole burning removes the broadening caused by magnetic fields from 13C nuclei and demonstrate that it can be used for magnetic-field-insensitive thermometry.