Non-enzymatic cholesterol oxidation products (COPs) are nowadays receiving increasing attention in food technology for their potential use as biomarkers of freshness and safety in raw materials and complex food matrices, as well as markers of cholesterol oxidation during the production and shelf-life of end products. Here reported is the investigation of how long three prototype milk chocolates containing whole milk powders (WMPs) of increasing shelf-lives (i.e. 20, 120, and 180 days), could be safely stored in the market by adopting the non-enzymatic COPs as a quality markers. In addition, the protective effect of two different primary packaging, sealed and unsealed ones, in mitigating the generation of non-enzymatic COPs in three prototype milk chocolates after 3, 6, 9, 12 months of shelf-life was assessed to simulate two real storage conditions. Quantifying oxysterols' levels by mass spectrometry, the oxygen impermeable packaging (PLUS) resulted to significantly quench the non-enzymatic COPs production up to 34% as to that found in the same product but with unsealed standard packaging (STD). This study represents one practical application of non-enzymatic COPs as a reliable tool for corrective strategies to prevent food oxidation.