Despite the growing interest in membrane filtration for biorefining of microalgae, few works have dealt with membrane regeneration after fouling by such specific vegetable products. The current procedure still requires large volumes of cleaning solutions, which leads to additional energy and water consumption with a substantial environmental impact. NaCl solutions have already been used in precleaning steps to enhance the cleaning of ultrafiltration membranes fouled by whey proteins. The aim of this work was to test this innovative procedure on membranes fouled by a representative emulsion of microalgae lipid extracts and to gain insight into how salt promotes changes in fouling organization. Polyethersulfone (PES)-based membranes with an average pore diameter of 0.1 µm were fouled by the emulsion, and then cleaned in several steps: water precleaning, NaCl precleaning, detergent cleaning and sodium hypochlorite polishing. Two salt concentrations (5 and 7.5 mM NaCl) and 2 temperatures (37.5 °C and 50 °C) were considered and compared to control experiments. The cleaning efficiency of NaCl solutions was evaluated based on the hydraulic cleaning efficiency (HCE). The 5 mM NaCl solution at 50 °C led to the best precleaning performance with an HCE of 80%. The subsequent cleaning step with detergent U115 removed the remaining fouling and achieved 100% HCE without the need for a NaClO-NaOH polishing step. The impact of salt on membrane fouling was then investigated by characterizing the surface of the (i) pristine (ii) fouled and (iii) precleaned membranes with NaCl. Fouling was shown to occur on the surface of the membranes as well as in their porous structure, and to be irregularly organized in regions containing greater or lesser amounts of lipids. The use of NaCl significantly reduced internal fouling by moving lipids from the inside of the pores to the outer surface, thus facilitating the detergent cleaning step. This work contributes to the development of cost-effective and environmentally friendly cleaning procedures for separation processes used in many fields among which microalgae biorefinery.