Methods and systems for performing non-contact temperature measurements of optical elements with long wavelength infrared light are described herein. The optical elements under measurement exhibit low emissivity to long wavelength infrared light and are often highly reflective or highly transmissive to long wavelength infrared light. In one aspect, a material coating having high emissivity, low reflectivity, and low transmission at long wavelength IR wavelengths is disposed over selected portions of one or more optical elements of a metrology or inspection system. The locations of the material coating are outside the direct optical path of the primary measurement light employed by the metrology or inspection system to perform measurements of a specimen. Temperature measurements of the front and back surfaces of an IR-transparent optical element are performed with a single IR camera. Temperature measurements are performed through multiple optical elements in an optical path of a primary measurement beam.