The discovery of the phagocyte NADPH oxidase NOX2 went hand in hand with the elucidation of the phagocytes’ mechanism to kill microorganisms. It took decades to put together the pieces of the puzzle, then identify the enzyme responsible for phagosomal production reactive oxygen species (ROS) and its central role in our antimicrobial defence. How ROS actually kill the microbes is not fully understood. This chapter reviews the pieces of the puzzle and the potential ROS targets in microorganisms as well as their response to resist killing. The organisms that resist best cause major, sometimes life-threatening, infections. Understanding their means to resist and discovering their weak points remains challenging. Phagocytes employ numerous synergistic anti-microbial mechanisms, including ROS production. Experimental models only partially reflect this synergy. They also struggle to reproduce the complex dynamic chemistry of the phagosome. The difficulties to quantify phagosomal ROS illustrate the complexity of the task for future experiments. Different strains of bacteria and fungi employ distinct means to escape killing. New experimental approaches shall unravel the mechanism of escape and provide new ideas for infection therapeutics. In the future, we may help our natural immune response by weakening the antioxidant response of the pathogen.