We address the angular misalignment calibration problem, which arises when a multi-antenna GNSS serves as a source of aiding information for inertial sensors in an integrated navigation system. Antennas usually occupy some outside structure of the moving carrier object, whilst an inertial measurement unit typically remains inside. Especially when using low- or mid-grade MEMS gyroscopes and accelerometers, it is either impossible or impractical to physically align IMU-sensitive axes and GNSS antenna baselines within some 1–3 degrees due to the micromechanical nature of the inertial sensors: they are just too small to have any physical reference features to align to. However, in some applications, it is desirable to line up all sensors within a fraction-of-a-degree level of accuracy. One may imagine solving this problem via the long-term averaging of sensor signals in different positions to ensure observability and then using angle differences for analytical compensation. We suggest faster calibration in special rotations using sensor fusion. Apart from quicker convergence, this method also accounts for run-to-run inertial sensor bias instability. In addition, it allows further on-the-fly finer calibration in the background when the navigation system performs its regular operation, and carrier objects may undergo gradual deformations of its structure over the years.