Abstract This paper aims to develop and test Bayesian belief network-based diagnosis methods, which can be used to predict the most likely degradation levels of turbine, compressor, and fuel cell (FC) in a hybrid system based on different sensors measurements. The capability of the diagnosis systems to understand if an abnormal measurement is caused by a component degradation or by a sensor fault is also investigated. The data used both to train and to test the networks are generated from a deterministic model and later modified to consider noise or bias in the sensors. The application of Bayesian belief networks (BBNs) to fuel cell—gas turbine hybrid systems is novel, thus the results obtained from this analysis could be a significant starting point to understand their potential. The diagnosis systems developed for this work provide essential information regarding levels of degradation and presence of faults in a gas turbine, fuel cell and sensors in a fuel cell—gas turbine hybrid system. The Bayesian belief networks proved to have a good level of accuracy for all the scenarios considered, regarding both steady-state and transient operations. This analysis also suggests that in the future a Bayesian belief network could be integrated with the control system to achieve safer and more efficient operations of these plants.