An accurate knowledge of the unsteady aerodynamic forces acting on a bio-inspired, flapping-wing micro air vehicle (FWMAV) is crucial in the design development and optimization cycle. Two different types of experimental approaches are often used: determination of forces from position data obtained from external optical tracking during free flight, or direct measurements of forces by attaching the FWMAV to a force transducer in a wind-tunnel. This study compares the quality of the forces obtained from both methods as applied to a 17.4 gram FWMAV capable of controlled flight. A comprehensive analysis of various error sources is performed. The effects of different factors, e.g., measurement errors, error propagation, numerical differentiation, filtering frequency selection, and structural eigenmode interference, are assessed. For the forces obtained from free flight experiments it is shown that a data acquisition frequency below 200 Hz and an accuracy in the position measurements lower than ± 0.2 mm may considerably hinder determination of the unsteady forces. In general, the force component parallel to the fuselage determined by the two methods compares well for identical flight conditions; however, a significant difference was observed for the forces along the stroke plane of the wings. This was found to originate from the restrictions applied by the clamp to the dynamic oscillations observed in free flight and from the structural resonance of the clamped FWMAV structure, which generates loads that cannot be distinguished from the external forces. Furthermore, the clamping position was found to have a pronounced influence on the eigenmodes of the structure, and this effect should be taken into account for accurate force measurements.