The Estate of Castelporziano (Rome, Italy) hosts many ecosystems representative of Mediterranean vegetation, especially holm oak and pine forests and dune vegetation. In this work, basal emission factors (BEFs) of biogenic volatile organic compounds (BVOCs) obtained by Eddy Covariance in a field campaign using a proton transfer reaction-time-of-flight-mass spectrometer (PTR-TOF-MS) were compared to BEFs reported in previous studies that could not measure fluxes in real-time. Globally, broadleaf forests are dominated by isoprene emissions, but these Mediterranean ecosystems are dominated by strong monoterpene emitters, as shown by the new BEFs. The original and new BEFs were used to parametrize the model of emissions of gases and aerosols from nature (MEGAN v2.1), and model outputs were compared with measured fluxes. Results showed good agreement between modeled and measured fluxes when a model was used to predict radiative transfer and energy balance across the canopy. We then evaluated whether changes in BVOC emissions can affect the chemistry of the atmosphere and climate at a regional level. MEGAN was run together with the land surface model (community land model, CLM v4.0) of the community earth system model (CESM v1.0). Results highlighted that tropospheric ozone concentration and air temperature predicted from the model are sensitive to the magnitude of BVOC emissions, thus demonstrating the importance of adopting the proper BEF values for model parametrization.