Pressure-driven membrane processes are often used for the separation and purification of organic compounds originating from biomass. However, membrane fouling remains a challenge as these bio-based streams have a very complex composition and comprise a high fouling tendency. Conventional, the fouling is monitored based on either a decrease in flux or an increase in pressure over time. Those conventional techniques provide no information on the location, composition or amount of fouling. As fouling is often cumulative, it will be detected as a loss of performance. Once fouling becomes irreversible, it is often not possible to clean the membrane without chemicals and the filtration/separation process has to be stopped eventually. In situ real-time monitoring of membrane fouling could provide dynamic information on the development of fouling allowing optimization of the process. This paper reviews the state of the art in in situ monitoring techniques that could be applied to membrane processes in the biotechnology, biorefinery and food sectors and briefly reflects on the current awareness of in situ monitoring techniques among experienced industrial users of membrane processes. The physical principles as well as the strengths and weaknesses are addressed, as well as potentially and promising techniques are identified.