Carbon export driven by submesoscale, eddy-associated vertical velocities (“eddy subduction”) remains understudied, leaving a gap in our understanding of ocean carbon sequestration. Here, we assess mechanisms controlling eddy subduction’s spatial and seasonal patterns using 15 years of observations from BGC-Argo floats in the Southern Ocean. We identify signatures of eddy subduction as subsurface anomalies in temperature-salinity and oxygen. The anomalies’ spatial distribution is concentrated near weakly stratified areas and strong lateral buoyancy gradients diagnosed from satellite altimetry, particularly in the Antarctic Circumpolar Current’s standing meander regions. Meanwhile, vertical stratification drives seasonal variability. Bio-optical proxies associated with subsurface anomalies (such as the Chlorophyll a to particulate backscatter ratio: Chl/bbp), indicate that eddy subduction is most active in the spring and early summer, with freshly exported material associated with seasonally weak vertical stratification. Climate change is increasing ocean stratification globally, which may weaken eddy subduction’s carbon export potential.