The most widespread wood species in the Portuguese forest and the most widely utilized are maritime pine (Pinus pinaster) and eucalyptus (Eucalyptus globulus Labill). In the case of eucalyptus, except for the pulping sector, it might have limited usage due to drying issues and low permeability. Microwave (MW) treatment is a technology that has been used to improve wood species’ permeability. Therefore, the present paper aimed to evaluate the MW treatment of both Portuguese wood species and to investigate the effects of different MW treatments on wood’s density, water uptake capability, modulus of rupture (MOR), and modulus of elasticity (MOE). Using small clear wood specimens, two MW powers were used, 700 and 1200 W, and the samples were submitted to successive MW cycles of 2 min till they reached the required dryness. The results showed that each wood species had a different behavior during the MW drying in terms of drying rate, supply, and consumption of energy. In general, with the increase in MW power, the densities of both species decreased and the water uptake increased, as a possible indicator that a certain level of microstructural damage might have occurred. Regarding the mechanical properties of MW-treated maritime pine and eucalyptus wood specimens, under the harshest conditions (MW power of 1200 W), MOR and MOE were reduced compared with the wood sample without MW treatment.