To improve the shelf-life of food products rich in lipids, it is important to minimize the lipid oxidation that occurs during processing, since this oxidation not only decreases shelf-life but also induces off-flavors. To evaluate the oxidation of lipids in the production of one β-glucan-rich and one protein-rich food supplement made from oats (Avena sativa), the neutral and polar lipid profile, hexanal content, peroxide value, avenanthramides and lipase activity were measured at all production steps. The concentration of antioxidants in the form of avenanthramides was also investigated. This study shows that oat lipases were fully inactivated in the wet processing part of the processing line, and the total lipid content per dry weight increased with the progression of steps toward the oat protein product. Processing had no apparent effect on avenanthramide levels. Lipid oxidation markers increased in certain processing steps. The most significant increase in hexanal and peroxide values could be seen in the spray-drying step of the process, while a much smaller increase was seen for the drum-drying. The main conclusion is that the most important factor to prolong the shelf-life of the product is to minimize the oxidation in the drying step.