Recent nutritional studies have shown that the regular consumption of olive pomace oil (OPO) contributes to cardiovascular and cardiometabolic disease prevention. OPO could be a healthier alternative to the polyunsaturated oils employed in a number of bakery foods. However, little is known about the quality and nutritional changes of OPO in these products, especially the amounts of its bioactive components that finally reach consumers. The aim of this research was to evaluate refined OPO as a substitute for sunflower oil (SO) in cupcakes specially manufactured with a 6-month shelf-life. The influence of processing and storage on lipid oxidative changes and the levels of OPO bioactive components was studied. OPO samples exhibited much higher resistance to oxidative degradation in the processing and especially after storage, which had a greater oxidative impact. OPO reduced considerably the levels of oxidised lipids. HPLC analysis showed hydroperoxide triglyceride concentrations of 0.25 (±0.03) mmol/kg fat against 10.90 (±0.7) mmol/kg in the control containing SO. Sterols, triterpenic alcohols and triterpenic acids remained unchanged, and only slight losses of squalene (8 wt%) and α-tocopherol (13 wt%) were observed in OPO after processing and storage, respectively. Therefore, OPO preserved its nutritional properties and improved the quality and nutritional value of the cupcakes.