This paper investigates fault diagnosis in batch processes and presents a comparative study of feature extraction and classification techniques applied to a specific biotechnological case study: the fermentation process model by Birol et al. (Comput Chem Eng 26:1553-1565, 2002), which is a benchmark for advanced batch processes monitoring, diagnosis and control. Fault diagnosis is achieved using four approaches on four different process scenarios based on the different levels of noise so as to evaluate their effects on the performance. Each approach combines a feature extraction method, either multi-way principal component analysis (MPCA) or multi-way independent component analysis (MICA), with a classification method, either artificial neural network (ANN) or support vector machines (SVM). The performance obtained by the different approaches is assessed and discussed for a set of simulated faults under different scenarios. One of the faults (a loss in mixing power) could not be detected due to the minimal effect of mixing on the simulated data. The remaining faults could be easily diagnosed and the subsequent discussion provides practical insight into the selection and use of the available techniques to specific applications. Irrespective of the classification algorithm, MPCA renders better results than MICA, hence the diagnosis performance proves to be more sensitive to the selection of the feature extraction technique.