Magnetic circular dichroism (MCD) is demonstrated for the first time in substoichiometric molybdenum oxide (MoO 3−x ) nanoarchitectures to explore the origin of their near-IR (NIR) transitions. Various nanostructures of MoO 3−x are synthesized by a simple hydrothermal process using an ionic Mo(VI) or metallic Mo(0) precursor. The phase, morphology, and spectroscopic properties of the obtained nanostructures are dependent both on the reaction temperature and the molybdenum precursor. In particular, hexagonal MoO 3−x nanostructures are colored blue with different degrees. To better understand the nature of the electronic states in these nanomaterials, MCD spectroscopy is conducted. A derivative-like MCD response is detected in the vis-NIR region, but it is not attributed to surface magnetoplasmonic modes because of the absence of the peak-energy shift with the increasing refractive index of the dispersion medium. Then, the bisignate MCD signal can be attributed to Faraday B-terms for small-polaronic transitions, arising from two interacting polaronic states close in energy that would give opposite signs under an applied magnetic field. We believe that MCD evaluation for polaronic nanomaterials will expand promising new applications in fields such as semiconductor-based nanophotonics and magneto-optical devices.