In clinical movement biomechanics, kinematic data are often depicted as waveforms (i.e. signals), characterising the motion of articulating joints. Clinically meaningful interpretations of the underlying joint kinematics, however, require an objective understanding of whether two different kinematic signals actually represent two different underlying physical movement patterns of the joint or not. Previously, the accuracy of IMU-based knee joint angles was assessed using a six-degrees-of-freedom joint simulator guided by fluoroscopy-based signals. Despite implementation of sensor-to-segment corrections, observed errors were clearly indicative of cross-talk, and thus inconsistent reference frame orientations. Here, we address these limitations by exploring how minimisation of dedicated cost functions can harmonise differences in frame orientations, ultimately facilitating consistent interpretation of articulating joint kinematic signals. In this study, we present and investigate a frame orientation optimisation method (FOOM) that aligns reference frames and corrects for cross-talk errors, hence yielding a consistent interpretation of the underlying movement patterns. By executing optimised rotational sequences, thus producing angular corrections around each axis, we enable a reproducible frame definition and hence an approach for reliable comparison of kinematic data. Using this approach, root-mean-square errors between the previously collected (1) IMU-based data using functional joint axes, and (2) simulated fluoroscopy-based data relying on geometrical axes were almost entirely eliminated from an initial range of 0.7°–5.1° to a mere 0.1°–0.8°. Our results confirm that different local segment frames can yield different kinematic patterns, despite following the same rotation convention, and that appropriate alignment of reference frame orientation can successfully enable consistent kinematic interpretation.