The role of Secondary Biogenic Organic Aerosol in aerosol budget is examined using the Atmospheric Dispersion of Pollutants over Complex Terrain–Urban Airshed Model–Aerosols (ADREA‐I/UAM‐AERO) modeling system in two representative Mediterranean areas. The areas have been selected, because of their elevated biogenic emission levels and the sufficient degree of meteorological and land use diversity characterizing the locations. Comparison of the model results with and without biogenic emissions reveals the significant role biogenic emissions play in modulating ozone and aerosol concentrations. Biogenic emissions are predicted to affect the concentrations of organic aerosol constituents through the reactions of terpenes with O3, OH and NO3. The ozonolysis of terpenes is predicted to cause an increase in OH radical concentrations that ranges from 10% to 78% for Athens, and from 20% to 95% for Marseilles, depending on the location, compared to the predictions without biogenic emissions. The reactions of this extra hydroxyl radical with SO2 and NOx have as final products increased concentrations of sulfates and nitrates in the particulate phase. As a result, biogenic emissions are predicted to affect the concentrations not only of organic aerosols, but those of inorganic aerosols as well. Thus biogenic emissions should be taken into consideration when models for the prediction and enforcement of abatement strategies of atmospheric pollution are applied.