The main goal of this work is to design a supervising controller able to detect an anomaly in the milling process and implement the soultion in Field Programmable Gate Array (FPGA) chip. Executing this task, the controller continuously monitors the vibration signal coming from the acceleration sensor, installed on the milling machine, and striving to isolate new vibration patterns which are different from typical patterns recorded for the correct milling process. The detection method relies on determining selected signal features in the frequency domain and applying an auto-associative neural network (AANN) for novelty detection. It has been shown that by exercising the frequency spectrum of the vibration signal, extracting specific features of the signal's spectrum, and using an auto-associative neural network, it is possible to detect anomalies in a milling process with relatively high efficiency. The accuracy, sensitivity, specificity, precision, and false alarm rate are equal to 94.3, 100, 91.2, 88.9, and 8.8 percent. All necessary calculations can be accomplished by the developed single-chip FPGA embedded supervising controller. The controller allows high-speed calculations under low power consumption. It characterizes high reliability and low price compared to typically encountered solutions.