Detection of aerodynamic instabilities in compressors is of great importance for machine safety and efficiency. It is a challenge due to their highly non-stationary and non-linear character. In this study, a method of instability detection in centrifugal compressor employing empirical mode decomposition (EMD) is proposed. The method has proven to work well in isolating and highlighting features of instabilities from highly non-stationary, non-linear and noisy pressure signals. Two Instability Detection Features (IDFs) based on energy of selected intrinsic mode functions (IMFs) were defined for detection of inlet recirculation (IDF-IR) and surge (IDF-S). Two level classification is offered by the proposed method. The first allows to differentiate stable and unstable working conditions. The second distinguishes between two types of flow instability: local - inlet recirculation and global - surge. The proposed method was evaluated using short, high-frequency pressure signals collected for known operating conditions. Accuracy of inlet recirculation detection reached 100%, while detection of surge was 99% accurate. The EMD-based instabilities detection method has a traceable connection with the physics of the flow, thus it is fully explainable and should perform similarly well for different machines and measurement systems if appropriate IMFs are employed.