The effects of temperature and atmosphere (air and O 2) on the doping of monolayers of graphene (Gr) on SiO 2 and Si substrates, and on the doping of MoS 2 multilayer flakes transferred on the same substrates have been investigated. The investigations were carried out by in situ micro-Raman spectroscopy during thermal treatments up to 430 C, and by atomic force microscopy (AFM). The spectral positions of the G and 2D Raman bands of Gr undergo only minor changes during treatment, while their amplitude and full width at half maximum (FWHM) vary as a function of the temperature and the used atmosphere. The thermal treatments in oxygen atmosphere show, in addition to a thermal effect, an effect attributable to a p-type doping through oxygen. The thermal broadening of the line shape, found during thermal treatments by in situ Raman measurements, can be related to thermal phonon effects. The absence of a band shift results from the balance between a red shift due to thermal effects and a blue shift induced by doping. This shows the potential of in situ measurements to follow the doping kinetics. The treatment of MoS 2 in O 2 has evidenced a progressive erosion of the flakes without relevant spectral changes in their central zone during in situ measurements. The formation of MoO 3 on the edges of the flakes is observed indicative of the oxygen-activated transformation.