In the last decade, some wine producers have re‐evaluated the role of micro‐oxygenation guaranteed by the porosity of the earthenware in the fermentation and refinement phases and, thus, the potential and limitations of this technique on the flavour and aromatic profile of wine need further investigations. The wine volatile profile was analysed by headspace solid phase microextraction coupled with gas chromatography—mass spectrometry, and the volatile compound percentages in Sangiovese and Cabernet Franc vinified in Stainless Steel Containers and in amphorae over time were compared. Results showed that the in‐amphorae vinification enhances the aromatic components of the Cabernet Franc wine, while there is no substantial difference for Sangiovese wine. A metabolomic approach was also attempted for the first time, and the NMR analysis highlighted a difference between the spectra of the samples vinified in‐amphorae with respect to those vinified in steel suggesting a potential new approach to obtain a significant traceability.