The air fryer and the oven are common cooking methods in our daily lives. However, previous investigations of the air fryer were limited to its comparison with deep-fat frying. This study compared the differences between air frying and household oven baking (without a fan or other forced airflow inside) on food quality and physicochemical properties using a cupcake model. Results showed that the oven-baked cupcakes were softer in texture (87.15%), greener in color (6.07%), and lower in weight loss (7.78%) and toxic advanced glycation end products (AGEs, 21.40%) when the heating temperature and duration were the same as oven baking. To improve the sensory characteristics and health value, the cupcakes were fortified with green tea. The differences in texture, color, and level of toxicants between the two cooking methods were diminished after the addition of green tea. Moreover, the chemical profiles of green tea catechins in the green-tea-fortified cupcakes remained similar upon thermal cooking, except that the air-fried cupcakes were lower in gallic acid (GA) but higher in (−)-gallocatechin (GC). Collectively, based on the differences in heating mechanisms, our data indicated that oven baking is a better cooking method suitable to prepare cupcakes than air frying from the perspectives of sensory characteristics and food safety, while green tea additives effectively counter the drawbacks of the air fryer.