The monitoring of a membrane bioreactor (MBR) requires the assessment of both biological and membrane performance. Additionally, the development of membrane fouling and the requirements for frequent membrane cleaning are still major concerns during MBR operation, requiring tight monitoring and system characterization. Transmembrane pressure is usually monitored online and allows following the evolution of membrane performance. However, it does not allow distinguishing the fouling mechanisms occurring in the system or predicting the future behavior of the membrane. The assessment of the biological medium requires manual sampling, and the analyses involve several steps that are labor-intensive, with low temporal resolution, preventing real-time monitoring. Two-dimensional fluorescence spectroscopy is a comprehensive technique, able to assess the system status at real-time without disturbing the biological system. It provides large sets of data (system fingerprints) from which meaningful information can be extracted. Nevertheless, mathematical data analysis (such as machine learning) is essential to properly extract the information contained in fluorescence spectra and correlate it with operating and performance parameters. The potential of 2D fluorescence spectroscopy as a process monitoring tool for MBRs is, therefore, discussed in the present work in view of the actual knowledge and the authors’ own experience in this field.