Wheat germ (WG)’s shelf life after the milling process is incredibly short because of the presence of enzymes that aggravate the oxidation process; thus, stabilization is required in order to exploit the nutrients and bioactive compounds within WG. The critical point for the oxidation process is the mechanical treatment used to separate WG from the kernel, which exposes the lipid fraction to the air. Showing the connection between the quality of durum wheat, considering its storage management, and wheat germ oil (WGO), extracted with a cold press, solvent and supercritical CO2, is the aim of the study. The acidity and peroxide values were analyzed to evaluate lipid oxidation, while fatty acids, tocols, sterols and policosanols were evaluated for WGO characterization. The first fundamental step to control lipid oxidation is raw material management. Subsequently, the tempering phase of durum wheat, which is applied before the degermination process, is the most critical point for oxidation to develop because of the increase in moisture in the caryopsis and the activation of lipase and lipoxygenase. This represents a paradox: in order to stabilize the germ with degermination, first it seems inevitable to carry out a process that destabilizes it. To retains its highest quality, this will lead to a better use of the whole grain by reducing WG and by-product waste.