We present the first thermal infrared reflectance spectral characterization of moganite and mixtures of moganite with microcrystalline quartz. We find that for relatively high (>50%) abundances of moganite, the absolute reflectance for samples is significantly reduced. Using microscopic-Raman (~1 μm/pixel) measurements, we estimate the moganite content for various samples. We then compare Raman-derived moganite abundances with microscopic infrared reflectance (25 μm/pixel) spectra to determine the effects of increasing moganite abundance on thermal infrared spectra. We find that moganite is broadly spectrally similar to quartz with major reflectance maxima located between ~1030 and 1280 cm−1 and ~400 and 600 cm−1; but there are characteristic differences in the peak shapes, peak center positions, and especially the relative peak reflectance magnitudes. For regions with high (>50%) moganite content, the relative magntitudes of the reflectance maxima at 1157 and 1095 cm−1 (R1095/R1157 band ratio) can be used to estimate the moganite content. This work demonstrates the utility of thermal infrared microspectroscopy in isolating phases that are intimately mixed in a sample, and has applications in planetary science, where constituent phases of quartz-rich sedimentary rocks can be identified using remote or in situ thermal infrared spectroscopy.