Sodium hypochlorite (NaOCl) is widely used to remove biofouling in membrane bioreactors (MBRs) to recover the membrane performance. In this study, the effect of membrane cleaning with different NaOCl concentrations (0.01%, 0.1%, 1% and 10% of a stock solution containing 39.92g/L of free chlorine) on biofouling was investigated in a molasses based lab-scale MBR. Study of the bacterial biofilm community re-growth after six consecutive cleanings revealed that a minimal concentration of 0.1% NaOCl diminishes the bacterial richness and cell density on the membranes. ATR-FTIR analysis of the layer on the membrane surface revealed the presence of peaks associated with proteins and carbohydrates present in the biofouling layer and their intensity decreased after treatment with NaOCl. Analysis of the membrane performance by chemical oxygen demand (COD) measurement of the permeate and retentate showed that the rejection of the membranes after NaOCl chemical treatment was still high. The data showed that since NaOCl removes the bacterial biofilm and at the same time does not affect the membrane treatment performance, NaOCl can be recommended as a cleaning agent to remove biofouling in a lab-scale molasses based MBR.