The sensory and health properties of virgin olive oil (VOO) are highly related to its volatile and phenolic composition. Oxygen control in the pastes during malaxation may be a new technological parameter to regulate enzymatic activities, such as polyphenoloxidase, peroxidase, and lipoxygenase, which affect the phenolic and volatile composition of VOO. In this work, we monitored CO2 and O2 concentrations during industrial-scale olive paste malaxation with various initial O2 concentrations within the malaxer headspace. Results show that the O2 concentration in the malaxer headspace did not affect CO2 production during processing, whereas a strong influence was observed on the changes of the phenolic composition of olive pastes and VOOs, with high correlation coefficient for the total phenols (R = 0.94), especially for oleuropein and demethyloleuropein derivatives (R = 0.81). In contrast, aroma production during malaxation was minimally affected by the O2 concentration in the malaxer headspace.