Membrane separation processes (MSP) are widely used in various industries, but membrane fouling represents a significant challenge, affecting product quality and process performance. Effective cleaning and disinfection are crucial for reducing fouling, improving permeate quality, and extending membrane lifespan. Optimized cleaning protocols not only increase productivity but also reduce costs, energy consumption, and the need for supplementary products. Despite the recognized importance of these processes, there are gaps in scientific research addressing practical measures for both academic and industrial applications. This chapter highlights innovative methodological steps for membrane cleaning and disinfection, focusing on non-conventional processes and technological integration to improve the removal of contaminants. Additionally, operational conditions and precautions for enhancing cleaning performance are discussed based on theoretical guidelines. This chapter ultimately aims to advance the practical application of membrane cleaning methods, ensuring better product quality and membrane longevity.