Reducing the susceptibility of lipids to the oxidation process remains essential in food processing. In this regard, the present work assesses the role of vitrification in condensed gelatin/polydextrose systems on the oxidation of entrapped linolenic acid. The polymer based matrix was crosslinked with genipin at distinct levels to manipulate the physicochemical properties and glass transition phenomena. The former was assessed with Fourier transform infrared spectroscopy (FTIR), wide-angle X-ray diffraction (WAXD), and scanning electron microscopy (SEM). The latter was followed by differential scanning calorimetry (DSC) and small deformation dynamic oscillation in-shear. Hydroperoxide (ROOH) analysis was chosen as an expedient means of monitoring lipid oxidation, which it was performed over an extensive range of temperature (−10 to 50°C) and time (up to 3 days). ROOH development was assayed during the initiation, propagation and termination phase. Data modelling revealed a sigmoidal pattern of ROOH accumulation throughout the entire stage of lipid oxidation. Rate constants obtained in the initiation and propagation phase of oxidation demonstrate that the mechanical glass transition temperature is a critical parameter for the preservation of lipid components in high solid materials.