BACKGROUND: This study involved two commercial orchards located in Limarí Valley and Molina from two important Chilean production zones of extra virgin olive oil (EVOO). The investigation evaluated the effects of climate, soil composition, agricultural practices (fertilization and irrigation) and variety (considering two harvests) on the compounds responsible for the flavor of EVOO (volatiles and phenols) and how these compounds can explain the differences in chemical profiles by geographical origin, cultivar and fruit ripeness stage. RESULTS: Varieties from the Limarí Valley presented the highest content of phenolic compounds. A significant relationship (P < 0.05) between volatile compounds and climate indicated that the compounds produced via the lipoxygenase cascade were affected by the maximum temperature and, to a lesser extent, by evapo-transpiration and irrigation. The selection of different individual phenolic and volatile compounds independently allowed the significant differentiation of EVOOs, principally by geographical origin, crop season, fruit ripeness stage and, in a few cases, by cultivar. CONCLUSION: Soil and climate of the Chilean regions have much more influence than cultivars on the concentration of sensory quality compounds. Difference in latitude between orchards increases the importance of the geographical origin on the virgin olive oil chemical composition while full irrigation decreases the impact of the cultivar.