The supply of nutrients is a fundamental regulator of ocean productivity and carbon sequestration. Nutrient sources, sinks, residence times, and elemental ratios vary over broad scales, including those resulting from climate-driven changes in upper water column stratification, advection, and the deposition of atmospheric dust. These changes can alter the proximate elemental control of ecosystem productivity with cascading ecological effects and impacts on carbon sequestration. Here, we report multidecadal observations revealing that the ecosystem in the eastern region of the North Pacific Subtropical Gyre (NPSG) oscillates on subdecadal scales between inorganic phosphorus (Pi) sufficiency and limitation, when Pi concentration in surface waters decreases below 50–60 nmol⋅kg−1. In situ observations and model simulations suggest that sea-level pressure changes over the northwest Pacific may induce basin-scale variations in the atmospheric transport and deposition of Asian dust-associated iron (Fe), causing the eastern portion of the NPSG ecosystem to shift between states of Fe and Pi limitation. Our results highlight the critical need to include both atmospheric and ocean circulation variability when modeling the response of open ocean pelagic ecosystems under future climate change scenarios.