Centrifugal compressors are prone to aerodynamic instabilities, which are different flow structures detrimental to compressor efficiency and safety of operation. It has been shown that instabilities can be identified using a feature space approach, using processed historic data to define classes of operating conditions. A challenge lies in shaping the boundaries to ensure proper classification of new data, especially in the region of transition between instabilities. In this study, Gaussian process classification (GPC) is used as a classification enhancement for a centrifugal compressor instabilities detection system. GPC provides a probabilistic output that allows for investigating the probability distribution of each class and build flexible and adaptable boundaries between the classes. The performance of GPC is compared with another threshold approach from the literature. The results show that in the studied case, GPC is more accurate and provides higher flexibility in the transition zone but it can be prone to errors further away from the class boundaries