The concept of glass transition has been used in food products to study their stability, extending shelf life and enhancing organoleptic desirability. This investigation evaluates the effect of three-dimensional structure as a barrier to oxidation of omega fatty acids in condensed hydrocolloid-based matrices. Two high-solid preparations were employed: κ-carrageenan with glucose syrup and genipin-crosslinked gelatin with polydextrose. They supported discontinuous microscopic inclusions of linoleic and linolenic acids within the rubber-to-glass transition region of the condensed mixtures. Glass transition temperatures (Tg) were estimated using differential scanning calorimetry and in-shear dynamic oscillation. The rate of lipid oxidation was monitored by analysing hydroperoxide (ROOH) production during each oxidation phase. The structural transformation of the supporting matrices as a function of temperature significantly affects the oxidation processes. The mechanical or network Tg exhibited higher values than the calorimetric Tg, supporting reduced lipid oxidation rates by suppressing ROOH accumulation in the densified glassy matrices.