The air conditioning systems in electric city buses usually operate in rapidly changing ambient conditions and are more likely to suffer from mechanical faults. Although many fault detection and diagnosis (FDD) methods have been developed for building air conditioning systems, they are difficult to be applied to bus air conditioners since its operation is highly dynamic and fault-free data are usually unavailable. Therefore, this paper proposes an FDD method for electric bus air conditioners to tackle the above issues. First, the method identifies faults in an unsupervised manner by comparing selected features among a group of peer systems. Then, considering the features are influenced by the operating conditions, Gaussian process regression (GPR) models are established to find the relationships between each feature and its influential parameters. The probabilistic nature of the GPR is used to differentiate predictions with large uncertainty, which are then excluded from FDD. In this way, robustness of the method is evidently improved. Finally, fault indexes are defined to detect and diagnose mechanical faults. We applied the method to a group of air conditioners in a city bus fleet. Results showed that it can effectively identify refrigerant undercharge and indoor and outdoor fan problems with low false positive/genitive rates. Also, the method is highly robust and not sensitive to the faulty systems in the bus fleet.