• Principles and methods for fluorescence EEM are systematically outlined. • Fluorophore peak/region/component and energy information can be extracted from EEM. • EEM can fingerprint the physical/chemical/biological properties of DOM in MBRs. • EEM is useful for tracking pollutant transformation and membrane retention/fouling. • Improvements are still needed to overcome limitations for further studies. The membrane bioreactor (MBR) technology is a rising star for wastewater treatment. The pollutant elimination and membrane fouling performances of MBRs are essentially related to the dissolved organic matter (DOM) in the system. Three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy, a powerful tool for the rapid and sensitive characterization of DOM, has been extensively applied in MBR studies; however, only a limited portion of the EEM fingerprinting information was utilized. This paper revisits the principles and methods of fluorescence EEM, and reviews the recent progress in applying EEM to characterize DOM in MBR studies. We systematically introduced the information extracted from EEM by considering the fluorescence peak location/intensity, wavelength regional distribution, and spectral deconvolution (giving fluorescent component loadings/scores), and discussed how to use the information to interpret the chemical compositions, physiochemical properties, biological activities, membrane retention/fouling behaviors, and migration/transformation fates of DOM in MBR systems. In addition to conventional EEM indicators, novel fluorescent parameters are summarized for potential use, including quantum yield, Stokes shift, excited energy state, and fluorescence lifetime. The current limitations of EEM-based DOM characterization are also discussed, with possible measures proposed to improve applications in MBR monitoring.