While there has been considerable work examining the effect of malaxation time on different characteristics of olive oils, there have been few that deal with all the major aspects. Here, the influence of malaxation time was evaluated using major local Tunisian (cv. Chemlali and Chetoui) cultivars. Standard characteristics were measured as well as detailed analyses of volatile compounds were conducted. Headspace solid-phase microextraction (HS-SPME) was applied to the analysis of volatile compounds of virgin olive oils from Chemlali and Chetoui varieties with differing malaxation time. Twenty-seven compounds were characterised by GC-FID and GC–MS. Compounds belonging mainly to alcohols, esters, aldehydes, ketones and hydrocarbons chemical classes characterized the volatile profile. Significant differences in the proportion of volatiles from oils of different malaxation time were detected. The results suggest that besides genetic factors, malaxation time influences volatile formation. The main variables that were affected by malaxation time were the total amount of phenols and composition of the volatile compounds. At malaxation time of 30 min, Chemlali and Chetoui olive oils presented the highest total phenol content (244.19 and 877.63 mg kg−1, respectively), while the lowest content was observed at 60 min from regardless of cultivars. In turn, this influenced the oxidative stability and peroxide value. It was also clear that the cultivars behaved differently and this prevented general conclusions being made for all of the quality characteristics.