The selective photocatalytic oxidation with O2 as oxidant of valencene and thymol was evaluated using nanostructured TiO2 under UV-Vis radiation at atmospheric conditions. The effect of the morphology and optical properties of TiO2 nanotubes and aminate nanoparticles was studied. Different scavengers were used to detect the presence of positive holes (h+), electrons (e-), hydroxyl radicals (•OH), and the superoxide radical anion (O2-) during the photooxidation reaction. Superoxide anion radical is the main oxidizing specie formed, which is responsible for the selective formation of nootkatone and thymoquinone using aminated TiO2 nanoparticles under 400 nm radiation.