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Eastern Boundary Upwelling Systems (EBUSs) are coastal hotspots of the potent greenhouse gas nitrous oxide (N2O). However, estimates of their emissions suffer from large uncertainties due to their significant spatial and temporal heterogeneity. Here, we derive the first multiyear, monthly resolution N2O emissions from three of the four major EBUSs using high‐frequency coastal atmospheric measurements and an inverse method. We find average combined N2O emissions from the northern California, Benguela, and southern Canary upwelling systems to be 57.7 (51.4–63.9) Gg‐N yr−1. We also find an offshore region near the Benguela EBUS that exhibits large pulses of emissions with emissions that reach 677 Gg‐N yr−1 in 1 month. Our findings highlight that atmospheric measurements coupled with inverse modeling can capture the large variability in EBUS emissions by quantifying emissions over large spatial distances and over long time periods compared to previous methods using traditional oceanographic measurements. Plain Language Summary: Eastern Boundary Upwelling Systems (EBUSs) are important emissions hotspots of marine nitrous oxide to the atmosphere, where it acts as a greenhouse gas and ozone depleting substance. Emissions from the EBUSs are highly episodic, and most previous estimates are snapshots derived from ship‐based measurements. The variability in emissions combined with the sparsity of measurements makes EBUS emission estimates highly uncertain. Here, we use multiyear, near‐continuous atmospheric measurements from coastal stations and an inverse modeling framework to derive emissions from three of the four major EBUSs. Our results quantify the significant spatial and temporal variability in emissions, which is not well‐represented in global studies of marine nitrous oxide emissions. Key Points: Eastern Boundary Upwelling System (EBUS) N2O emissions are episodic, and methods are needed to capture their variability in space and timePrevious upscaled estimates of EBUS emissions based on sparse measurements may be inaccurateN2O emissions from the northern California upwelling system vary with PDO phase [ABSTRACT FROM AUTHOR]