Titanium dioxide films were grown on unheated substrates by mid‐frequency (100 kHz) reactive pulsed magnetron sputtering at different O2 partial pressures in an Ar/O2 atmosphere. X‐ray diffraction and absorption measurements reveal a transition from amorphous anatase to nanocrystalline rutile with [O2], with a mixture of both phases at intermediate values. Atomic force microscopy shows that the promotion of rutile is accompanied by surface roughening due to the apparition of hollow structures (holes) on the surface, in contrast with the extremely smooth morphology of amorphous anatase films. The number and size of holes increase with [O2] and growth time in such a way that they eventually coalesce and percolate to lead to a rough surface for those growth conditions for which a rutile rich film is obtained. Transmission electron microscopy analysis shows the growth evolution of a heterogeneous phase mixture and provides unambiguous correlation between the hole (smooth) morphology and the underlying rutile (anatase) phase. Therefore, the surface morphology results from the slower local growth rate of nanocrystalline rutile compared to that of the surrounding amorphous anatase flat regions as well as from the fast (slow) lateral (vertical) growth rate of the rutile domains.