A methodology based on Principal Component Analysis (PCA) and clustering is evaluated for process monitoring and process analysis of a pilot-scale SBR removing nitrogen and phosphorus. The first step of this method is to build a multi-way PCA (MPCA) model using the historical process data. In the second step, the principal scores and the Q-statistics resulting from the MPCA model are fed to the LAMDA clustering algorithm. This procedure is iterated twice. The first iteration provides an efficient and effective discrimination between normal and abnormal operational conditions. The second iteration of the procedure allowed a clear-cut discrimination of applied operational changes in the SBR history. Important to add is that this procedure helped identifying some changes in the process behaviour, which would not have been possible, had we only relied on visually inspecting this online data set of the SBR (which is traditionally the case in practice). Hence the PCA based clustering methodology is a promising tool to efficiently interpret and analyse the SBR process behaviour using large historical online data sets.