Modern oceans are characterized by large areas of oxygen deficient zone (ODZ with global dissolved oxygen concentration [O₂] less than 5 mmol kg^-1) in the Pacific and a negligible ODZ in the Atlantic. As global warming continues, it is often assumed that warmer climates will expand ODZs and lower global oxygen due to enhanced productivity and reduced oxygen solubility. However, Earth system model experiments indicate that although global dissolved O₂ initially drops, it subsequently increases on millennial timescales. In Miocene (5.3 to 23 Ma) simulations with an open Central American Seaway (CAS) and elevated CO₂, the Pacific ODZ contracts while the Atlantic ODZ emerges and expands. This spatial reorganization is likely driven by changes in ocean circulation and ventilation due to the opening of the CAS, which lead to enhanced water-column denitrification in the eastern Atlantic at the expense of the Pacific. Secondary contributions from wind-driven upwelling and elevated CO₂ further contribute to deoxygenation. Our findings also reveal a major shift in the marine N cycle under Miocene boundary conditions, including a rise in global N₂ fixation rates, a decrease in the ocean’s average δ¹⁵N values, and ~80% increase in benthic denitrification. These results highlight that tectonic-driven circulation changes, rather than warming alone, were the primary driver of Atlantic deoxygenation and nitrogen cycle perturbations during the Miocene, with implications for how future warming might impact regional OMZs.