Reflection high-energy electron diffraction (RHEED) is a powerful tool in molecular beam epitaxy (MBE), but RHEED images are often difficult to interpret, requiring experienced operators. We present an approach for automated surveillance of GaAs substrate deoxidation in MBE reactors using deep learning based RHEED image-sequence classification. Our approach consists of an non-supervised auto-encoder (AE) for feature extraction, combined with a supervised convolutional classifier network. We demonstrate that our lightweight network model can accurately identify the exact deoxidation moment. Furthermore we show that the approach is very robust and allows accurate deoxidation detection during months without requiring re-training. The main advantage of the approach is that it can be applied to raw RHEED images without requiring further information such as the rotation angle, temperature, etc.