Coenzyme Q10 is a potent antioxidant that plays an important role in the maintenance of various biochemical pathways of the body and has a wide range of therapeutic applications. However, it has low aqueous solubility and oral bioavailability. Mesoporous silica nanoparticles (MCM-41 and SBA-15 types) exhibiting varying pore sizes and modified with phosphonate and amino groups were used to study the influence of pore structure and surface chemistry on the solubility, in vitro release profile, and intracellular ROS inhibition activity of coenzyme Q10. The particles were thoroughly characterized to confirm the morphology, size, pore profile, functionalization, and drug loading. Surface modification with phosphonate functional groups was found to have the strongest impact on the solubility enhancement of coenzyme Q10 when compared to that of pristine and amino-modified particles. Phosphonate-modified MCM-41 nanoparticles (i.e., MCM-41-PO 3 ) induced significantly higher coenzyme Q10 solubility than the other particles studied. Furthermore, MCM-41-PO 3 led to a twofold decrease in ROS generation in human chondrocyte cells (C28/I2), compared to the free drug in a DMSO/DMEM mixture. The results confirmed the significant contribution of small pore size and negative surface charge of MSNs that enable coenzyme Q10 confinement to allow enhanced drug solubility and antioxidant activity.