Phenolic compounds largely contribute to the nutraceutical properties of virgin olive oil (VOO), the organoleptic attributes and the shelf life due to their antioxidant capabilities. Due to the relevance of malaxation in the oil extraction process, we tested the effects of malaxation time on the concentrations of relevant phenolic compounds in VOO, and we evaluated the influence of performing malaxation under vacuum. An increase in malaxation time significantly decreased the concentrations of aglycone isomers of oleuropein and ligstroside but, conversely, increased the oleocanthal and oleacein contents. Additionally, malaxation under vacuum led to an increase in phenolic contents compared to standard conditions carried out at atmospheric pressure. Finally, we explored the possibility of predicting the VOO oxidative stability on the basis of the phenolic profile, and a model (R² = 0.923; p < 0.0001) was obtained by combining the concentration of the VOO phenolic compounds and the main fatty acids.