The decomposition of organic matter slows at low oxygen (O₂) but implications of this phenomenon for ocean biogeochemical cycles are virtually unknown. Here we use an ocean biogeochemistry–ecosystem model to show that an empirically constrained O₂ sensitivity of particle remineralization has dramatic impacts on a suite of biogeochemical processes, from primary productivity to nitrogen (N) cycling, which are critical to marine ecosystems and carbon sequestration. The preservation of particles settling through the extreme O₂ minimum zones (OMZs) of the tropics decelerates global water-column denitrification and its coupling to N-fixation by more than 3-fold. This slower tropical N cycling allows homeostatic regulation of the ocean’s nitrogen to phosphorus ratio, preventing the exhaustion of bioavailable N in upwelling waters, a pervasive bias in Earth system models. It also reconciles the partition of N loss between OMZs and sediments with geochemical observations. While these effects prevent N depletion, they paradoxically reduce rates of N-limited tropical primary productivity by 40% due to the deepening of the nutricline. Ocean deoxygenation may exacerbate nutrient trapping in a warming and stratifying ocean, limiting productivity that sustains diverse ecosystems and fisheries.