In this paper, we present a comparative study of LIPSS formation on sub-stoichiometric titanium oxide thin films grown using pulsed laser deposition (PLD) and Magnetron Sputtering (MS). Irradiation was performed using femtosecond lasers beams, emitting at wavelengths 266 and 1030 nm, and at different numbers of laser pulses and laser fluences. Conditions for the formation of LIPSS were determined for both types of films, at 266 nm. A variety of nanostructures such as LSFL, HSFL, spikes, dots were detected and their shapes and sizes were found to strongly depend on laser fluence and number of pulses, as essentially dictated by free-surface energy minimization. LIPSS appeared to follow similar formation pattern for both PLD and MS films, except for some de lamination detected for the MS films. This was attributed to better adhesion and a lower stress state of the PLD films compared to their MS counterparts. Large surface nanostructuring experiments performed at 1030 nm showed less delamination with the increase of the laser fluence, resulting from a competition between the cracking and the melting of the layers.