In this work we have developed a prototype gaseous pixel detector by combining a micromegas grid with a Timepix3 chip for the readout. The micromegas foil supported by a matrix of pillars about 50 μm high was manually placed on top the chip. By placing a cathode foil above the chip an ionisation detector was created with a drift gap of 13.5 mm. The Timepix3 chip, thanks to the simultaneous measurement of the time-of-arrival (ToA) and charge via time-over-threshold (ToT) allows corrections to remaining timewalk effects, improving further the position resolution along the drift direction. We present the timewalk correction for Timepix3 chip obtained with real data from a particle beam and its impact on the tracking performance. The results obtained show a significant improvement on the position resolution for single-hits and tracks along the drift direction compared to previous experiments.