AbstractAerobic processes require oxygen, and anaerobic processes are typically hindered by it. In many places in the global ocean, oxygen is completely removed at mid‐water depths forming anoxic oxygen minimum zones (A‐OMZs). Within the oxygen gradients linking oxygenated waters with A‐OMZs, there is a transition from aerobic to anaerobic microbial processes. This transition is not sharp and there is an overlap between processes using oxygen and those using other electron acceptors. This review will focus on the oxygen control of aerobic and anaerobic metabolisms and will explore how this overlap impacts both the carbon and nitrogen cycles in A‐OMZ environments. We will discuss new findings on non‐phototrophic microbial processes that produce oxygen, and we focus on how oxygen impacts the loss of fixed nitrogen (as N2) from A‐OMZ waters. There are both physiological and environmental controls on the activities of microbial processes responsible for N2 loss, and the environmental controls are active at extremely low levels of oxygen. Understanding how these controls function will be critical to understanding and predicting how fixed‐nitrogen loss in the oceans will respond to future global warming.