This study evaluates the reliability and agreement of the 3D range of motion (ROM) of trunk and lower limb joints, measured by inertial measurement units (MVN BIOMECH Awinda, Xsens Technologies), during a single leg squat (SLS) and sit to stand (STS) task. Furthermore, distinction was made between movement phases, to discuss the reliability and agreement for different phases of both movement tasks. Twenty healthy participants were measured on two testing days. On day one, measurements were conducted by two operators to determine the within-session and between-operator reliability and agreement. On day two, measurements were conducted by the same operator, to determine the between-session reliability and agreement. The SLS task had lower within-session reliability and agreement compared with between-session and between-operator reliability and agreement. The reliability and agreement of the hip, knee, and ankle ROM in the sagittal plane were good for both phases of the SLS task. For both phases of STS task, within-session reliability and agreement were good, and between-session and between-operator reliability and agreement were lower in all planes. As both tasks are physically demanding, differences may be explained by inconsistent movement strategies. These results show that inertial sensor systems show promise for use in further research to investigate (mal)adaptive movement strategies.