The Southern Ocean plays a pivotal role in the global ocean circulation and climate1, 2, 3. There, the deep water masses of the world ocean upwell to the surface and subsequently sink to intermediate and abyssal depths, forming two overturning cells that exchange substantial quantities of heat and carbon with the atmosphere4, 5. The sensitivity of the upper cell to climatic changes in forcing is relatively well established6. However, little is known about how the lower cell responds, and in particular whether small-scale mixing in the abyssal Southern Ocean, an important controlling process of the lower cell7, 8, is influenced by atmospheric forcing. Here, we present observational evidence that relates changes in abyssal mixing to oceanic eddy variability on timescales of months to decades. Observational estimates of mixing rates, obtained along a repeat hydrographic transect across Drake Passage, are shown to be dependent on local oceanic eddy energy, derived from moored current meter and altimetric measurements. As the intensity of the regional eddy field is regulated by the Southern Hemisphere westerly winds9, 10, our findings suggest that Southern Ocean abyssal mixing and overturning are sensitive to climatic perturbations in wind forcing.