Dispersions of three different types of zirconia nanoparticles were treated in a stirred media mill. The deployed surface modifier was present during milling and it established separating mechanisms between the particles. The combination of mechanical deagglomeration and chemical surface modification results in stable zirconia colloids with average particle sizes down to 9 nm. In addition to deagglomeration, the milling treatment also causes comminution of nanoparticles. This was indicated for the two coarser types of the examined particles, by increasing surface areas and decreasing primary crystallite sizes. Transmission electron microscopy of the particles confirmed the creation of smaller primary crystallites and a minority of small fragments, but the majority of particles do not undergo comminution into halves or fragments with similar size. Changes of the particles’ phase composition, wear of milling media, amorphization of the particles to a small extent, and leaching of Y2O3dopant have been observed as side effects in the process and are characterized quantitatively. This work describes a process for nanoparticle deagglomeration and preparation of high quality colloids, and informs about occurring side effects, including approaches for their minimization.