Metal oxide nanoparticles have many useful applications in environmental studies, as tracking agents in life sciences, and in nutrient delivery for nano-enhanced agriculture. A key challenge in controlling the behavior of metal oxide nanoparticles in aqueous media is that molecular ligands are unstable with respect to hydrolytic cleavage from the surfaces. This instability limits the practical application of metal oxide nanoparticles in aqueous media. We have developed a method for producing nanometer-thin carbon shells on the surface of Al 2 O 3 , Cr 3+ :Al 2 O 3 (nanoruby), ZnO, and Fe 3 O 4 (magnetite) metal oxides that provides a scaffold for subsequent covalent chemical functionalization. Fluorescence measurements using carbonized Cr 3+ :Al 2 O 3 (nanoruby) confirm that these thin carbon coatings have relatively little impact on the optical properties, allowing bright emission with less than 50% decrease in fluorescence intensity compared to an identical nanoruby without carbon coating. We demonstrate the utility for functionalization by modifying C-coated Al 2 O 3 with molecular ligands bearing positive and negative charges. This approach provides a pathway for functionalization of a broad range of metal oxide nanoparticles with molecular ligands that can confer specific molecular properties to the nanoparticle surfaces in aqueous media while taking advantage of the high strength and stability of C−C interfacial bonds between surface ligands and the carbon shell.