Routine chemical cleaning with the combined use of sodium hydroxide (NaOH) and hydrochloric acid (HCl) is carried out as a means of biofouling control in reverse osmosis (RO) membranes. The novelty of the research presented herein is in the application of urea, instead of NaOH, as a chemical cleaning agent to full-scale spiral-wound RO membrane elements. A comparative study was carried out at a pilot-scale facility at the Evides Industriewater DECO water treatment plant in the Netherlands. Three fouled 8-inch diameter membrane modules were harvested from the lead position of one of the full-scale RO units treating membrane bioreactor (MBR) permeate. One membrane module was not cleaned and was assessed as the control. The second membrane module was cleaned by the standard alkali/acid cleaning protocol. The third membrane module was cleaned with concentrated urea solution followed by acid rinse. The results showed that urea cleaning is as effective as the conventional chemical cleaning with regards to restoring the normalized feed channel pressure drop, and more effective in terms of (i) improving membrane permeability, and (ii) solubilizing organic foulants and the subsequent removal of the surface fouling layer. Higher biomass removal by urea cleaning was also indicated by the fact that the total organic carbon (TOC) content in the HCl rinse solution post-urea-cleaning was an order of magnitude greater than in the HCl rinse after standard cleaning. Further optimization of urea-based membrane cleaning protocols and urea recovery and/or waste treatment methods is proposed for full-scale applications.