Oceanic cross-density (diapycnal) mixing helps sustain the ocean density stratification and its Meridional Overturning Circulation (MOC) and is key to global tracer distributions. The Southern Ocean (SO) is a key region where different overturning cells connect, allowing nutrient and carbon rich Indian and Pacific deep waters, and oxygen rich Atlantic deep waters to resurface. The SO is also rife with intense diapycnal mixing due to the interaction of energetic eddies and currents with rough topography. SO diapycnal mixing is believed to be of secondary importance for the MOC. Here we show that changes to SO mixing can cause significant alterations to biogeochemical tracer distributions over short and long time scales in an idealized model of the AMOC (Atlantic MOC). While such alterations are dominated by the direct impact of changes in diapycnal mixing on tracer fluxes on annual to decadal time scales, on centennial time scales they are dominated by the mixing-induced variations in the advective transport of the tracers by the AMOC. This work suggests that an accurate representation of spatio-temporally variable local and non-local mixing processes in the SO is essential for climate models’ ability to (i) simulate the global biogeochemical cycles and air sea carbon fluxes on decadal time scales, (ii) represent the indirect impact of mixing-induced changes to AMOC on biogeochemical cycles on longer time scales.