The present-day marine nitrogen (N) cycle is strongly regulated by biology. Deficiencies in the availability of fixed and readily bioavailable nitrogen relative to phosphate (P) in the surface ocean are largely corrected by the activity of diazotrophs. This feedback system, termed the “nitrostat”, is thought to have provided close regulation of fixed N speciation and inventory relative to P since the Proterozoic. In contrast, during intervals of intense deoxygenation such as Cretaceous Ocean Anoxic Event (OAE) 2, a few regional sedimentary δ15N records hint at the existence of a different mode of marine N-cycling in which ammonium plays a major role in regulating export production. However, the global-scale dynamics during this time remain unknown. Here, using an Earth System model and taking the example of OAE 2, we provide new insights into the global marine nitrogen cycle under severe ocean deoxygenation. Specifically, we find that the ocean can exhibit fundamental transitions in the species of nitrogen dominating the fixed N inventory – from nitrate (NO3-) to ammonium (NH4+) – and that as this transition occurs, the inventory can partially collapse relative to P due to progressive spatial decoupling between the loci of NH4+ oxidation, NO3- reduction, and nitrogen fixation. This finding is relatively independent of the specific state of ocean circulation and is consistent with nitrogen isotope and redox proxy data. The substantive reduction in the ocean fixed N inventory at an intermediate state of deoxygenation may represent a biogeochemical vulnerability with potential implications for past and future (warmer) oceans.