This study explores the application of various machine learning (ML) models for the real-time prediction of the FOS/TAC ratio in microbial electrolysis cell anaerobic digestion (MEC-AD) systems using data collected during a 160-day trial treating brewery wastewater. This study investigated models including decision trees, XGBoost, support vector regression, a variant of support vector machine (SVM), and artificial neural networks (ANNs) for their effectiveness in the soft sensing of system stability. The ANNs demonstrated superior performance, achieving an explained variance of 0.77, and were further evaluated through an out-of-fold ensemble approach to assess the selected model's performance across the complete dataset. This work underscores the critical role of ML in enhancing the operational efficiency and stability of bio-electrochemical systems (BES), contributing significantly to cost-effective environmental management. The findings suggest that ML not only aids in maintaining the health of microbial communities, which is essential for biogas production, but also helps to reduce the risks associated with system instability.