Climate variability and climate change in Eastern Boundary Upwelling Systems (EBUS) affect global marine ecosystems services. We use passive tracers in a global ocean model hindcast at eddy-permitting resolution to diagnose EBUS low-frequency variability over 1958-2015 period. The results highlight the uniqueness of each EBUS in terms of drivers and climate variability. The wind forcing and the thermocline depth, which are potentially competitive or complementary upwelling drivers under climate change, control EBUS low-frequency variability with different contributions. Moreover, Atlantic and Pacific upwelling systems are independent. In the Pacific, the only coherent variability between California and Humboldt Systems is associated with El Niño Southern Oscillation. The remaining low-frequency variance is partially explained by the North and South Pacific expressions of the Meridional Modes. In the Atlantic, coherent variability between Canary and Benguela Systems is associated with upwelling trends, which are not dynamically linked and represent different processes. In the Canary, a negative upwelling trend is connected to the Atlantic Multi-decadal Oscillation, while in the Benguela, a positive upwelling trend is forced by a global sea level pressure trend, which is consistent with the climate response to anthropogenic forcing. The residual variability is forced by localized offshore high sea level pressure variability.