The aim of this project was to identify the characteristic flavor and off-flavor compounds that could be used as potential oxidation markers to establish the quality of the stored wines and to predict the wines’ shelf life employing a mathematical model. Six mono-varietal Greek white wines (produced by three varieties) were bottled using two types of corks having different oxygen permeability properties. Volatile compounds, resistance to oxidative degradation and total and free-sulfur dioxide content were recorded in all samples. Results were processed using the root cause analysis versus packaging and storage conditions. Additionally, a predictive model has been constructed to estimate the shelf life of the bottled wine. Physicochemical analysis indicated the absence of significant oxidative degradations during the first 7 months. Furthermore, 12-month stored samples showed a significant alteration in their flavor profile. Based on the concentration of the selected oxidation marker (isoamyl-alcohol), the possibility of the bottled product not reaching the end of its shelf life, has been used to quantify the product’s quality. A very successful fit was achieved between mathematical and experimentally obtained data concerning shelf life predictions. The modeling of the results indicated the importance of cork selection due to the Oxygen Transmission Rate (OTR) values that potentially impact the quality of the wines in time, according to the evolution of the isoamyl-alcohol concentration. For the wine industry, the selection of the appropriate cork according to the wine type is an important consideration.