This study aims to explore the potential for accurately estimating joint angles during upper limb rehabilitation tasks with different calibration procedures, inverse kinematics methods and measurement modalities. Affordable embedded visual-inertial measurement units offer a promising alternative to the costly and cumbersome gold standard marker-based stereophotogrammetric systems. However, affordability comes with inherent sensors inaccuracies. Hence, prior to their application in a real clinical setting, it is important to demonstrate their ability for accurate joint angle estimation. Discrepancies in joint angles arise due to the inaccuracies of different sensing modalities but also to sensor-to-segment calibration procedures that significantly alter the joint offsets. Therefore, in this paper, the impact of functional and anatomical calibration procedures on joint angle estimation was compared among seven healthy young volunteers. When the same calibration procedures were applied with visual-inertial measurement units and stereophotogrammetric systems data, a relatively small root mean square error of 7.9deg and correlation coefficients exceeding 0.86 were observed. When different calibration procedures were applied with visual-inertial measurement units and stereophotogrammetric systems data, higher root mean square superior to 10deg were observed, highlighting the importance of consistency with the reference set when assessing accuracy. Furthermore, our analysis shows the benefit of using multi-body inverse kinematics procedure over treating inverse kinematics separately for each segment when dealing with inaccurate visual-inertial measurement units data.