Polydopamine (PDA) materials are important due to their unique physicochemical properties and their potential as chemopreventive agents for diseases connected with oxidative stress. Although PDA has been suggested to display antioxidant activity, its efficacy is controversial and its mechanism of action is still unclear. Herein, we report that accurately purified PDA nanoparticles in water at pH 7.4 are unable to quench alkylperoxyls (ROO˙), which are the radicals responsible for the propagation of lipid peroxidation, despite PDA reacting with the model DPPH˙ and ABTS˙⁺ radicals. PDA nanoparticles prepared by copolymerization of dopamine with the dialkyl nitroxide 4-NH₂TEMPO show instead good antioxidant activity, thanks to the ROO˙ trapping ability of the nitroxide. Theoretical calculations performed on a quinone–catechol dimer, reproducing the structural motive of PDA, indicate a reactivity with ROO˙ similar to catechol. These results suggest that PDA nanoparticles have an “onion-like” structure, with a catechol-rich core, which can be reached only by DPPH˙ and ABTS˙⁺, and a surface mainly represented by quinones. The importance of assessing the antioxidant activity by inhibited autoxidation studies is also discussed.