Gel filtration is a versatile technique employed for biological molecules and nanoparticles, offering their reproducible classification based on size and shape. Colloidal nanoparticles are of significant interest in biomedical applications due to a large number of solution-based bioconjugation procedures. Nevertheless, the inherent polydispersity of the nanoparticles produced by various techniques necessitates the employment of high yield separation and purification techniques. Here we demonstrate the employment of gel filtration on non-stoichiometric plasmonic MoO x nanoparticles, prepared by an oxidation process during liquid-phase exfoliation of few-layer MoS2 nanosheets. This resulted in the separation of two types of MoO x particles, in the form of two different chromatographic fractions. They showed different sizes, morphological and optical properties. The fraction containing smaller particles with diameters of 1-4 nm, exhibited an increased absorbance peak in the near IR region and responded with a significant temperature increase to laser irradiation at the wavelength close to the maximal absorption. The fraction with the larger particles from 3 up to 10 nm, showed weak photoluminescence and a preferred orientation upon the deposition on a planar substrate. However, it had no absorbance in the near IR compared to the former fraction. According to our knowledge, this is the first time that the gel filtration was applied to the separation of molybdenum oxide nanomaterials. This step ensured the isolation of plasmonic MoO x nanoparticles suitable for further bioconjugation and target photothermal treatment.