Current cleaning strategies for biofouling control on spiral wound membrane systems used for seawater desalination are not effective and can hinder long-term membrane performance. To enable effective cleaning of a membrane, we examined the in-situ application and the use of a sacrificial multilayer polyelectrolyte coating on the membrane surface. The membrane coating was based on a layer-by-layer assembly approach using two non-toxic linkers, poly (diallyl-dimethyl ammonium chloride) and poly(sodium-4-styrene sulfonate). This polyelectrolyte coating was effectively applied on the membrane surface under cross-flow conditions, and it was stable on the membrane surface under continuous operation. Coating removal requires only a concentrated sodium chloride solution (synthetic brine in our study) adjusted to pH 11. Using this procedure, both the biofilm and the sacrificial layer could be simultaneously removed, leaving a clean surface compared to the non-coated membrane. Biofouling tests showed that the coated membrane had two-fold higher permeate flux recovery than the control non-coated membrane. The used polyelectrolyte sacrificial coatings avoided the use of toxic linkers and harsh cleaning chemicals, and thus it is a suitable technique for biofouling control on reverse osmosis spiral wound membranes.