Abstract Antarctic‐origin abyssal waters occupy a significant fraction of the global ocean volume and play a key role in deep circulation and ventilation, yet their volume is declining rapidly in a warming climate. Although the Indian Ocean (IO) contains a substantial fraction of these waters, abyssal pathways and upwelling in the basin remain poorly understood due to sparse observations. Here, we investigate abyssal transports using an eddy‐resolving regional ocean model. We find the abyssal waters flooding the IO along three distinct pathways with a net northward transport of ∼12.5 Sv across 32° $32{}^{circ}$S, consistent with observational estimates. For the first‐time, we identify regional hot‐spots of large‐scale abyssal upwelling that occur along ridges and continental boundaries, transferring ∼10 Sv of abyssal waters upward, of which ∼8 Sv returns southward as deep waters. These results provide new constraints on the structure and closure of the lower limb of the IO overturning circulation.