Reactive oxygen and nitrogen species as well as advanced glycation endproducts (AGEs) and metalloproteinases (MMPs) play a key role in the development and progression of degenerative processes of body tissues, including skin. Natural antioxidant flavonoids could be beneficial in inhibiting AGEs’ formation and MMPs’ expression. In this study, the antioxidant activity of flavones (luteolin, apigenin, and chrysin) and flavonols (mirycetin, quercetin, and kaempferol) was compared with their inhibitory effects on both metalloproteinases’ (MMP-1, MMP-2, MMP-9, MMP-13) and AGEs’ formation. Comparisons were performed taking into account the hydroxyl group arrangement and the physico-chemical parameters the binding dissociation enthalpy (BDE), ionization potential (IP), partition coefficient (log P), and topological polar surface area (TPSA). Increasing the number of hydroxyl groups led to a proportional enhancement of antioxidant activity while an inverse relationship was observed plotting the antioxidant activity vs. BDE and IP values. All flavonoids acted as AGEs, MMP-1, and MMP-13 inhibitors, but they were less effective against MMP-2 and MMP-9. The inhibition of MMP-1 seemed to be related to the TPSA values while high TPSA and low log P values seemed important conditions for inhibiting MMP-13. Overall, our data suggest that an estimation of flavonoid activity could be anticipated based on their physico-chemical parameters.