Frantoio olive fruits were stored at low temperature (4 ± 2 °C) for 3 weeks to investigate the effect of post-harvest fruit storage on virgin olive oil quality. Volatile compounds and phenolic compounds explained the changes in sensory quality that could not be explained with quality indices (FFA, PV, K232 and K270). Increase in concentrations of (E)-2-hexenal and hexanal corresponded to positive sensory quality whereas increase in (E)-2-hexenol and (+)-acetoxypinoresinol was associated with negative sensory quality. Volatile and phenolic compounds were also indicative of the period of low temperature fruit storage. Oleuropein and ligstroside derivatives in olive oil decreased with respect to storage time and their significant (p<0.05) change corresponded to changes in bitterness and pungency. (Z)-2-penten-1-ol increased during low temperature fruit storage whereas 2-pentyl furan decreased. Changes in volatile compounds, phenolic compounds, quality indices, and sensory notes indicated that virgin olive oil quality was lost within the first week of low temperature fruit storage and re-gained at two weeks. Our research suggests that low temperature olive fruit storage may be beneficial, with a possibility of increasing oil yield and moderating the sensory quality of virgin olive oils. This study demonstrates that deeper insights into virgin olive oil quality changes during low temperature fruit storage may be gained by studying volatile and phenolic compounds in addition to quality indices and physical appearance of the fruit.