Size-controlled PtRu nanoparticles embedded in WO3 were prepared by simultaneous multigun sputtering on pure targets of Pt, Ru, and WO3. The mean diameter of the PtRu nanoparticles, as confirmed by high-resolution transmission electron microscopy, can be varied from -2.3 to -3.6 nm by varying the RF power ratio of PtRu and WO3. On the basis of transmission electron diffraction results for the PtRu nanoparticles embedded in WO3, it was confirmed that PtRu exists as an alloy metal phase, whereas the WO3 matrix is present as an amorphous phase. Size-controlled PtRu/WO3 electrodes were found to exhibit unique electronic properties depending on their size, which affected the potential of zero total charge and the methanol oxidation reaction. The mass activity of PtRu/WO3 for methanol oxidation was determined by the interplay of the surface electronic factors at the metal-solution interface; the oxophilicity of the nanoparticles increased with decreasing particle size.