The quality of virgin olive oil (VOO) is strictly related to the concentrations of phenolic and volatile compounds, which are strongly affected by the operative conditions of the VOO mechanical extraction process. The aim of this work is to study the impact of a new technology such as flash thermal conditioning (FTC) on olive paste structural modification and on VOO quality. The evaluation of olive paste structure modification by cryo-scanning electron microscopy (cryo-SEM) showed that the application of FTC after crushing produces significant differences in terms of the breaking of the parenchyma cells and aggregation of oil droplets in comparison to the crushed pastes. The virgin olive oil flash thermal conditioning (VOO-FTC) featured a higher concentration of volatile compounds compared to that in the control, particularly of all saturated and unsaturated aldehydes and esters, whereas the phenolic concentration was higher in VOO obtained from the traditional process (VOO-C).