In this work, a new custom design of an anomaly detection and classification system is proposed. It is composed of a convolutional Auto-Encoder (AE) hardware design to perform anomaly detection which cooperates with a mixed HW/SW Convolutional Neural Network (CNN) to perform the classification of detected anomalies. The AE features a partial binarization, so that the weights are binarized while the activations, associated to some selected layers, are non-binarized. This has been necessary to meet the severe area and energy constraints that allow it to be integrated on the same die as the MEMS sensors for which it serves as a neural accelerator. The CNN shares the feature extraction module with the AE, whereas a SW classifier is triggered by the AE when a fault is detected, working asynchronously to it. The AE has been mapped on a Xilinx Artix-7 FPGA, featuring an Output Data Rate (ODR) of 365 kHz and achieving a power dissipation of 333 W/MHz. Logic synthesis has targeted TSMC CMOS 65 nm, 90 nm, and 130 nm standard cells. Best results achieved highlight a power consumption of 138 μW/MHz with an area occupation of 0.49 mm 2 when real-time operations are set. These results enable the integration of the complete neural accelerator in the CMOS circuitry that typically sits with the inertial MEMS on the same silicon die. Comparisons with the related works suggest that the proposed system is capable of state-of-the-art performances and accuracy.