•Incubation effect of GaN at 1030, 515 and 343 nm.•Micromachining threshold fluence of GaN.•Fs-laser micromachining of GaN. This paper presents a study on the incubation effect during fs-laser micromachining of gallium nitride films with three different wavelengths (1030, 515 and 343 nm) by varying the number of laser pulses applied per sample surface area and measuring the damage threshold fluence using the zero damage method. As we implemented the exponential defect accumulation model to the experimental incubation data, we determined the value of the incubation parameter of (0.02 ± 0.01) for 1030 nm, (0.07 ± 0.01) for 515 nm and (0.4 ± 0.1) for 343 nm. This shows that for excitation in the green and infrared spectral region, GaN requires approximately 100 overlapping pulses in order for the incubation to take place while, for ultraviolet excitation, the incubation was achieved faster, with the overlap of about 10 pulses. Furthermore, we compared our data for the single pulse damage threshold with a theoretical model that takes into account multiphoton and avalanche ionization. Our results indicate that at 343 nm and 515 nm, micromachining is dominated by multiphoton ionization, while at 1030 nm other effects, such as tunneling ionization, must also be contributing. Finally, we believe this paper brings relevant information on the fs-laser micromachining of GaN.