Methods of cleaning and sanitizing membrane modules within a membrane system are provided. A cleaning solution is circulated through the membrane system for about 2 to about 30 minutes. The cleaning solution includes organic acid and surfactant. A sanitizing solution is added to the cleaning solution to produce a boosted antimicrobial solution comprising an oxidizer. The boosted antimicrobial solution is then circulated through the membrane system for about 1 to about 20 minutes. The methods described are effective for reducing and removing bacterial spores and biofilms from membranes and improving membrane compatibility of effective cleaning and sanitizing solutions.