This paper presents a novel approach to address noise, vibration, and harshness (NVH) issues in electrically assisted bicycles (e-bikes) caused by the drive unit. By investigating and optimising the structural dynamics during early product development, NVH can decisively be improved and valuable resources can be saved, emphasising its significance for enhancing riding performance. The paper offers a comprehensive analysis of the e-bike drive unit’s mechanical interactions among relevant components, culminating—to the best of our knowledge—in the development of the first high-fidelity model of an entire e-bike drive unit. The proposed model uses the principles of elastic multi body dynamics (eMBD) to elucidate the structural dynamics in dynamic-transient calculations. Comparing power spectra between measured and simulated motion variables validates the chosen model assumptions. The measurements of physical samples utilise accelerometers, contactless laser Doppler vibrometry (LDV) and various test arrangements, which are replicated in simulations and provide accessibility to measure vibrations onto rotating shafts and stationary structures. In summary, this integrated system-level approach can serve as a viable starting point for comprehending and managing the NVH behaviour of e-bikes.