MitoQ(10) is a ubiquinone that accumulates within mitochondria driven by a conjugated lipophilic triphenylphosphonium cation (TPP(+)). Once there, MitoQ(10) is reduced to its active ubiquinol form, which has been used to prevent mitochondrial oxidative damage and to infer the involvement of reactive oxygen species in signaling pathways. Here we show MitoQ(10) is effectively reduced by complex II, but is a poor substrate for complex I, complex III, and electron-transferring flavoprotein (ETF):quinone oxidoreductase (ETF-QOR). This differential reactivity could be explained if the bulky TPP(+) moiety sterically hindered access of the ubiquinone group to enzyme active sites with a long, narrow access channel. Using a combination of molecular modeling and an uncharged analog of MitoQ(10) with similar sterics (tritylQ(10)), we infer that the interaction of MitoQ(10) with complex I and ETF-QOR, but not complex III, is inhibited by its bulky TPP(+) moiety. To explain its lack of reactivity with complex III we show that the TPP(+) moiety of MitoQ(10) is ineffective at quenching pyrene fluorophors deeply buried within phospholipid bilayers and thus is positioned near the membrane surface. This superficial position of the TPP(+) moiety, as well as the low solubility of MitoQ(10) in non-polar organic solvents, suggests that the concentration of the entire MitoQ(10) molecule in the membrane core is very limited. As overlaying MitoQ(10) onto the structure of complex III indicates that MitoQ(10) cannot react with complex III without its TPP(+) moiety entering the low dielectric of the membrane core, we conclude that the TPP(+) moiety does anchor the tethered ubiquinol group out of reach of the active site(s) of complex III, thus explaining its slow oxidation. In contrast the ubiquinone moiety of MitoQ(10) is able to quench fluorophors deep within the membrane core, indicating a high concentration of the ubiquinone moiety within the membrane and explaining its good anti-oxidant efficacy. These findings will facilitate the rational design of future mitochondria-targeted molecules.