The effect of blanketing with CO2, naturally evolved during malaxation of olive pastes, on the quality of virgin olive oil was investigated at lab-scale. The O2 depletion was monitored along with CO2 emission to confirm the previously hypothesized accelerated respiration. Malaxation experiments were conducted for 180 min both in sealed (SC) and in the traditional open-to-air conditions to ascertain whether the oil quality was affected by O2 concentration as afforded by CO2 blanketing. The quality of olive oils obtained at different time intervals was monitored by total acidity, peroxide value (PV), specific extinction coefficients K232 and K270, total chlorophyll and total hydrophilic phenols, and HPLC hydrophilic phenols profile. A rapid decrease in oxygen concentration and a simultaneous increase in CO2 concentration were recorded, confirming the accelerated respiration. The oil produced in SC showed a lower PV and K232 coefficient and a higher chlorophyll (10–17 mg/kg) and hydrophilic phenols (110 mg/kg) concentration. No differences in total acidity and K270 coefficient were observed. The hydrophilic phenols profile indicated that, at least for the Frantoio cultivar and an advanced ripeness state, the maximal extraction is generally achieved already after 20 min. Most of the individual hydrophilic phenols have higher concentrations (up to 50%) in SC.