Biogenic volatile organic compounds play important roles in atmospheric chemistry, and their emissions can be greatly influenced by the variations in environmental conditions and physiological activities caused by continuously increasing global nitrogen (N) deposition. However, this influence is still poorly understood, especially in a natural ecosystem. We conducted a one-year (2015-2016) experiment adding N deposition (60 kg N ha−1) with fertilization to a Mediterranean shrubland dominated by Erica multiflora and a Mediterranean forest dominated by Quercus ilex and compared the seasonal and daytime photosynthetic rates (A), stomatal conductances (gs) and rates of isoprenoid emission with control (2015-2016) and pre-treatment (2014-2015) plots. N fertilization increased A in warm weather as soil moisture increased, and assimilation became saturated when the environment was sufficiently favorable, and excess soil N significantly restrained A in cold weather. The plants were much more sensitive to soil water availability than N content and terpene emissions increased synergistically due to heat and drought stress in hot weather. N fertilization did not significantly affect isoprene emission but significantly increased total terpene emissions and decreased the diversity of terpenes. Our results suggest a successful acclimation of plants by emitting more isoprenoids under environmental stress and that N deposition will further stimulate emissions as the Mediterranean region becomes warmer and drier. The results highlight the necessity for predicting the most realistic future of ecosystems under global environmental change and for assessing the impacts of multiple factors acting in concert on plant physiological and ecosystem functioning including biogenic VOC emissions.