Inertial capture (InCap) systems combined with musculoskeletal (MSK) models are an attractive option for monitoring 3D joint kinematics in an ecological context. However, the primary limiting factor is the sensor-to-segment calibration, which is crucial to estimate the body segment orientations. Walking, running, and stair ascent and descent trials were measured in eleven healthy subjects with the Xsens InCap system and the Vicon 3D motion capture (MoCap) system at a self-selected speed. A novel integrated method that combines previous sensor-to-segment calibration approaches was developed for use in a MSK model with three degree of freedom (DOF) hip and knee joints. The following were compared: RMSE, range of motion (ROM), peaks, and R2 between InCap kinematics estimated with different calibration methods and gold standard MoCap kinematics. The integrated method reduced the RSME for both the hip and the knee joints below 5°, and no statistically significant differences were found between MoCap and InCap kinematics. This was consistent across all the different analyzed movements. The developed method was integrated on an MSK model workflow, and it increased the sensor-to-segment calibration accuracy for an accurate estimate of 3D joint kinematics compared to MoCap, guaranteeing a clinical easy-to-use approach.