Flow visualisations are essential to better understand the unsteady aerodynamics of flapping wing flight. The issues inherent to animal experiments, such as poor controllability and unnatural flapping when tethered, can be avoided by using robotic flyers that promise for a more systematic and repeatable methodology. Here, we present a new flapping-wing micro air vehicle (FWMAV)-specific control approach that, by employing an external motion tracking system, achieved autonomous wind tunnel flight with a maximum root-mean-square position error of 28 mm at low speeds (0.8-1.2 m/s) and 75 mm at high speeds (2-2.4 m/s). This allowed the first free flight flow visualisation experiments to be conducted with an FWMAV. Time-resolved stereoscopic particle image velocimetry was used to reconstruct the three-dimensional flow patterns of the FWMAV wake. A good qualitative match was found in comparison to a tethered configuration at similar conditions, suggesting that the obtained free-flight measurements are reliable and meaningful.