Dietary polyphenols have been proposed to be promising functional food additives for their potent antioxidant capacity and other health-beneficial bioactivities. The current study prepared cookies fortified with five selected dietary polyphenols (naringenin, quercetin, epicatechin, chlorogenic acid, and rosmarinic acid). Results indicated that the enhancement of the antioxidant capacity was not as obvious as expected because the phenolics' antioxidant activity was seriously lowered by the baking process due to thermal degradation and transformation. Meanwhile, the tested polyphenols, especially quercetin, showed inhibition against formation of both reactive carbonyl species and total fluorescent advanced glycation endproducts (AGEs). Polyphenol fortification could also induce colorimetric changes and alterations in selected quality attributes. Overall, the findings support dietary polyphenols as functional food ingredients in the purpose of health benefits associated with a higher intake of antioxidants and a lower load of reactive carbonyls and AGEs. The polyphenols' stability and reactivity during thermal processing should be an important consideration.