Portable measurement systems using inertial sensors enable motion capture outside the lab, facilitating longitudinal and large-scale studies in natural environments. However, estimating 3D kinematics and kinetics from inertial data for a comprehensive biomechanical movement analysis is still challenging. Machine learning models or stepwise approaches performing Kalman filtering, inverse kinematics, and inverse dynamics can lead to inconsistencies between kinematics and kinetics. We investigated the reconstruction of 3D kinematics and kinetics of arbitrary running motions from inertial sensor data using optimal control simulations of full-body musculoskeletal models. To evaluate the feasibility of the proposed method, we used marker tracking simulations created from optical motion capture data as a reference and for computing virtual inertial data such that the desired solution was known exactly. We generated the inertial tracking simulations by formulating optimal control problems that tracked virtual acceleration and angular velocity while minimizing effort without requiring a task constraint or an initial state. To evaluate the proposed approach, we reconstructed three trials each of straight running, curved running, and a v-cut of 10 participants. We compared the estimated inertial signals and biomechanical variables of the marker and inertial tracking simulations. The inertial data was tracked closely, resulting in low mean root mean squared deviations for pelvis translation (≤20.2mm), angles (≤1.8 deg), ground reaction forces (≤1.1 BW%), joint moments (≤0.1 BWBH%), and muscle forces (≤5.4 BW%) and high mean coefficients of multiple correlation for all biomechanical variables . Accordingly, our results showed that optimal control simulations tracking 3D inertial data could reconstruct the kinematics and kinetics of individual trials of all running motions. The simulations led to mutually and dynamically consistent kinematics and kinetics, which allows researching causal chains, for example, to analyze anterior cruciate ligament injury prevention. Our work proved the feasibility of the approach using virtual inertial data. When using the approach in the future with measured data, the sensor location and alignment on the segment must be estimated, and soft-tissue artifacts are potential error sources. Nevertheless, we demonstrated that optimal control simulation tracking inertial data is highly promising for estimating 3D kinematics and kinetics for a comprehensive biomechanical analysis.