This study investigates whether the 3-D wind vector can be measured reliably from a highly transportable and low-cost weight-shift microlight aircraft. We draw up a transferable procedure to accommodate flow distortion originating from the aircraft body and -wing. This procedure consists of the analysis of aircraft dynamics and seven successive calibration steps. For our aircraft the horizontal wind components receive their greatest single amendment (14%, relative to the initial uncertainty) from the correction of flow distortion magnitude in the dynamic pressure computation. Conversely the vertical wind component is most of all improved (31%) by subsequent steps considering the 3-D flow distortion distribution in the flow angle computations. Therein the influences of the aircraft’s trim (53%), as well as changes in the aircraft lift (16%) are considered by using the measured lift coefficient as explanatory variable. Three independent lines of analysis are used to evaluate the quality of the wind measurement: (a) A wind tunnel study in combination with the propagation of sensor uncertainties defines the systems input uncertainty to ≈0.6ms^-1 at the extremes of a 95% confidence interval. (b) During severe vertical flight manoeuvres the deviation range of the vertical wind component does not exceed 0.3ms^-1. (c) The comparison with ground based wind measurements yields an overall operational uncertainty (root mean square error) of ≈0.4ms^-1 for the horizontal and ≈0.3ms^-1 for the vertical wind components. No conclusive dependence of the uncertainty on the wind magnitude (<8ms^-1) or true airspeed (ranging from 23–30ms^-1) is found. Hence our analysis provides the necessary basis to study the wind measurement precision and spectral quality, which is prerequisite for reliable eddy-covariance flux measurements.