Pinus radiata (PR) and Eucalyptus globulus (EG) are the most planted species in Chile. This research aims to evaluate the pyrolysis behaviour of PR and EG from the Bío Bío region in Chile. Biomass samples were subjected to microwave pretreatment considering power (259, 462, 595, and 700 W) and time (1, 2, 3, and 5 min). The maximum temperature reached was 147.69 °C for PR and 130.71 °C for EG in the 700 W-5 min condition, which caused the rearrangement of the cellulose crystalline chains through vibration and an increase in the internal energy of the biomass and the decomposition of lignin due to reaching its glass transition temperature. Thermogravimetric analysis revealed an activation energy (Ea) reduction from 201.71 to 174.91 kJ·mol−1 in PR and from 174.80 to 158.51 kJ·mol−1 in EG, compared to the untreated condition (WOT) for the 700 W-5 min condition, which indicates that microwave pretreatment improves the activity of the components and the decomposition of structural compounds for subsequent pyrolysis. Functional groups were identified by Fourier transform infrared spectroscopy (FTIR). A decrease in oxygenated compounds such as acids (from 21.97 to 17.34% w·w−1 and from 27.72 to 24.13% w·w−1) and phenols (from 34.41 to 31.95% w·w−1 and from 21.73 to 20.24% w·w−1) in PR and EG, respectively, was observed in comparison to the WOT for the 700 W-5 min condition, after analytical pyrolysis. Such results demonstrate the positive influence of the pretreatment on the reduction in oxygenated compounds obtained from biomass pyrolysis.