Our study investigated the degradation mechanisms of dark chocolate bars with hazelnut paste. Through comprehensive characterization analyses, we assessed porosity, polyphenols, fatty acids, Hesanal, dicarbonyl compounds, metabolic profile, and moisture content. Building on these findings, we developed an antioxidant solution to modify chocolate’s degradation and preserve natural flavors. By integrating this solution into flexible packaging, we aim to extend shelf life and enhance the sensory experience.