The production of a high quality product requires good manufacturing practices and effective quality assurance throughout the whole process. The aim of this study was to improve the knowledge of the technological variables involved in the malaxation operation, which affect the yield and in particular the overall quality of the virgin olive oil. A continuous experimental virgin olive oil mill plant (Pieralisi, Fattoria) was employed, working at 200 kg/h olive paste, and the paste was kneaded at different temperatures (20–40 °C) and times (30–90 min). The industrial oil yield improved when either the kneading temperature or the kneading time was increased, but the temperature affected more the oil yield than the time (yield increased by about 28%, from 20 to 40 °C). The total phenol and o-diphenol contents in virgin olive oils, which affect both the sensory bitterness and the oxidative stability of the oils, greatly improved with the increase in the malaxation temperature. On the contrary, a longer kneading time only led to a slight decrease in the total phenols. This fact is very important since excessive levels of phenols, typical of Cornicabra virgin olive oils, may adversely affect consumer preference for this highly valued product.