Determining the State-of-Health (SoH) of fuel cell systems during operation is vital for implementing model-based control strategies that aim to minimize degradation and extend the fuel cell lifetime. This paper introduces a novel observer architecture designed to estimate the internal states as well as the SoH of fuel cell systems in real time. The proposed observer offers three key advantages: (1) it decouples the dynamics of internal states from SoH, thus enhancing numerical stability, (2) by incorporating multiple measurement points, assessing the SoH for various components within the fuel cell (e.g. membrane, catalyst layer) becomes possible, and (3) in combination with the used physical real-time capable model, the observer architecture facilitates real-time evaluation of the SoH during dynamic operation. The observer’s benefits are demonstrated through simulations and measurement data.