Membrane biofouling poses a serious challenge in reverse osmosis (RO) plants used for water recovery, which cannot be addressed by traditional chlorine-based cleaning agents. To accommodate this problem and enhance membrane performance while maintaining high-quality water production, various cleaning strategies have been applied. It remains however challenging to identify optimal cleaning agents, as tests require discontinuation of production to evaluate the effect. This study introduces a self-formed instrument that mimics industrial RO plants on a small scale to compare the cleaning agents in a fast, affordable and feasible approach. The setup was demonstrated using three cells operating in parallel and a thorough comparison of these. Specifically, the online cleaning efficiency of a typical biofouling cleaner, a solution of NaOH/sodium dodecyl sulfate (SDS), and the commonly used non-oxidizing biocide, 2,2-dibromo-3-nitrilopropionamide, were compared to validate the system performance when fed with membrane bioreactor effluent. The effectiveness of the cleaning process was evaluated using a combination of hydrodynamic operation and membrane autopsy to estimate the biofoulant amount and composition. During a 7-day operating period, it was observed that treated membranes demonstrated higher flux rates compared to untreated membranes. The normalized flux increased more than double in the membrane after it had been cleaned with NaOH/SDS solution. CLSM analysis clearly showed the distinct effects of the two cleaning solutions on the amount and spatial structure of the biofilm layer. Cleaning with DBNPA was able to reduce the load of living bacteria, but not necessarily remove the biofilm components completely. Comparative analyses of membranes revealed that NaOH/SDS exhibited the highest cleaning efficiency during the online cleaning operation mode. This benchmark highlights the versatility of the system, which can be assembled at relevant sites and assist in the identification of efficient and eco-friendly agents that promote the lifespan of membranes. With the distribution of this instrument, it will be possible to accelerate the investigation of multiple cleaning strategies and also analyze interactions among cleaning agents in an attempt to reduce water shortage.