The controlled growth of self-assembled second-phase nanostructures has been shown to be an essential tool for enhancing properties of several composite oxide thin film systems. Here, the role of Y2O3 nanoparticles on the growth of BaZrO3 (BZO) nanorods is investigated in order to understand the mechanisms governing their self-assembly in YBa2Cu3O7–x (YBCO) thin films and to more fully control the resulting defect landscape. By examining the microstructure and current-carrying capacity of BZO-doped YBCO films, it is shown that the nanorod growth dynamics are significantly enhanced when compared to films double-doped with BZO and Y2O3 nanoparticles. The average nanorod length and associated critical current densities are found to increase at a significantly higher rate in the absence of Y2O3 nanoparticles when the growth temperature is increased. Using microstructural data from transmission electron microscopy studies and the response in critical current density, the interactive effects of multiple dopants that must be considered to fully control the defect landscape in oxide thin films are shown.