Carotenoids are essential components in the human diet due to their positive functions in ocular and cognitive health. This study investigated composition of carotenoids in hairless canary seed (HCS) as a novel food and the effect of baking on carotenoids in bread and muffin made from HCS, wheat and corn. Three bread formulations made from wheat and HCS blends were evaluated and compared with control wheat bread. In addition, three low-fat muffin recipes prepared from HCS alone or in blends with corn were assessed. The fate of carotenoid compounds in breads and muffins was monitored after dry mixing, dough/batter formation and oven baking. Carotenoids in products were quantified using UPLC and their identification was confirmed based on LC-MS/MS. Hairless canary seed and corn were fairly rich in carotenoids with a total content of 7.6 and 12.9 µg/g, respectively, compared with wheat (1.3 µg/g). Nineteen carotenoid compounds were identified, with all-trans lutein being the principal carotenoid in HCS followed by lutein 3-O-linoleate, lutein 3-O-oleate and lutein di-linoleate. There were significant reductions in carotenoids in muffin and bread products. It appears that batter or dough preparation causes more reductions in carotenoids than oven baking, probably due to enzymatic oxidation and degradation. Muffin-making resulted in lower lutein reductions compared with the bread-making process. The results suggest that muffins made from hairless canary seed alone or in blends with corn could boost the daily intake of lutein and/or zeaxanthin.