Hazelnuts are characterized by a relatively high abundance of oleic acid and poly-unsaturated fatty acids, which give this fruit a high nutritional value. As a counterbalance, such a lipid profile is more susceptible to autoxidation and/or degradation reactions under enzymatic catalysis. Lipid oxidation occurs on fatty acids (FAs), both esterified on triacylglycerols and in free form (after lipolysis), but with favorable kinetics on the latter. In this study, the quali-quantitative changes in FA profiles (both free and esterified) were monitored during the shelf life (time 0, 6, and 12 months) as a function of different drying and storage conditions and different cultivars and geographical areas. A derivatization/extraction procedure was performed to quantify the profile of free and esterified fatty acids accurately. The overall profile of the free and esterified fatty acids concurred to create a biological signature characteristic of the cultivar and of the harvest region. The free and esterified forms’ characterization enabled the efficient monitoring of the effects of both the hydrolytic activity (increment in overall free fatty acids) and the oxidative process (decrease in unsaturated free fatty acids versus esterified fatty acids) over the 12 months of storage.