In commercial terms, Extra Virgin Olive Oil (EVOO) is considered an exceptional food with excellent sensory and nutritional quality due to its taste, odor, and bioactive compounds; as such, it is of great health interest. This quality can be affected by the oxidative degradation, both chemical and enzymatic (the activity of oxidative, endogenous enzymes from the polyphenol oxidase and peroxidase olive fruit type), of essential components during the extraction and conservation of EVOO. In the bibliography, oxygen reduction during the malaxation process and oil storage has been studied in different ways. However, research concerning oxygen reduction in the crushing of the olive fruit or the malaxation of the paste, or both, in the “real extraction condition” is scarce. Oxygen reduction has been compared to control conditions (the concentration of atmospheric oxygen (21%)). Batches of 200 kg of the olive fruit, ‘Picual’ cultivar, were used and the following treatments were applied: Control (21% O2Mill–21% O2Mixer), “IC-NM”: Inerted crushing -Normal malaxation (6.25% O2Mill-21% O2Mixer), “NC-IM”: Normal crushing-Inerted malaxation (21% O2Mill-4.39% O2Mixer) and “IC-IM”: Inerted crushing -Inerted malaxation (5.5% O2Mill-10.5% O2Mixer). The parameters of commercial quality covered by regulation (free acidity, peroxide value and absorbency in ultra-violet (K232and K270)) did not suffer any change concerning the control, and so the oils belong to the commercial category of “Extra Virgin Olive Oil”. The phenolic compounds of the olives involved in the distinctive bitter and pungent taste, health properties, and oxidative stability are increased with the downsizing amounts of oxygen in the IC-NM, NC-IM, and IC-IM treatments with an average of 4, 10, and 20%, respectively. In contrast, the total amount of volatile compounds decreases by 10–20% in all oxygen reduction treatments. The volatile compounds arising from the lipoxygenase pathway, which are responsible for the green and fruity notes of EVOO, also decreased in concentration with the treatments by 15–20%. The results show how oxygen reduction in the milling and malaxation stages of olive fruit can modulate the content of phenols, volatile compounds, carotenoids, and chlorophyll pigments in the EVOO to avoid the degradation of the compound with sensorial and nutritional interest.