Flaxseed meal, rich in water-soluble gums, improves the texture of gluten-free (GF) products. Bioactive antioxidant peptides from flaxseed, known as linusorbs (LOs) or cyclolinopeptides, may provide health benefits. However, the stability of flaxseed-derived LOs during dough preparation, baking, and storage remains unclear. To investigate this, GF bread dough and bread were prepared with flaxseed meal, and the LO content was determined in the flaxseed meal, the bread flour with the flaxseed meal, the dough, and the bread. The LO levels were also monitored during storage at various temperatures (-18 °C, 4 °C, and 22-23 °C) for 0, 1, 2, and 4 weeks using high-performance liquid chromatography-diode array detection (HPLC-DAD). The levels of oxidized LOs, such as [1-9-NαC],[1-(<i>R</i>_s,<i>S</i>_s)-MetO]-linusorb B2 (LO<b>14</b>), remained relatively stable in the flaxseed meal and the flour derived from it across under all conditions for up to 4 weeks. Due to microbial contamination, the dough could not be stored at either 4 or 21 °C, and the bread could only be stored at 21 °C for one week. However, the bread and dough could be stored for up to 4 weeks at -18 °C, and the bread at 4 °C, without a significant loss of LOs. The main changes in LOs occurred during processing rather than storage. Reduced LOs were found in higher concentrations in the flour and meal compared to the dough and bread, without a corresponding increase in oxidized LOs. The flaxseed meal-fortified bread maintained oxidative stability when stored at low temperatures. This is the first study to investigate the effect of baking conditions on LO content and antioxidant properties.