Paleoclimate records from glacial Indian and Pacific oceans sediments document millennial-scale fluctuations of subsurface dissolved oxygen levels and denitrification coherent with North Atlantic temperature oscillations. Yet the mechanism of this teleconnection between the remote ocean basins remains elusive. Here we present model simulations of the oxygen and nitrogen cycles that explain how changes in deepwater subduction in the North Atlantic can cause large and synchronous variations of oxygen minimum zones throughout the Northern Hemisphere of the Indian and Pacific oceans, consistent with the paleoclimate records. Cold periods in the North Atlantic are associated with reduced nutrient delivery to the upper Indo-Pacific oceans, thereby decreasing productivity. Reduced export production diminishes subsurface respiration of organic matter leading to higher oxygen concentrations and less denitrification. This effect of reduced oxygen consumption dominates at low latitudes. At high latitudes in the Southern Ocean and North Pacific, increased mixed layer depths and steepening of isopycnals improve ocean ventilation and oxygen supply to the subsurface. Atmospheric teleconnections through changes in wind-driven ocean circulation modify this basin-scale pattern regionally. These results suggest that changes in the Atlantic Ocean circulation, similar to those projected by climate models to possibly occur in the centuries to come because of anthropogenic climate warming, can have large effects on marine ecosystems and biogeochemical cycles even in remote areas.