The initial rise in atmospheric CO2 during the last deglaciation was likely driven by input of carbon from a 13C-depleted reservoir. Here we show that high resolution benthic foraminiferal records from the mid-depth Brazil Margin display an abrupt drop in δ13C during Heinrich Stadial 1 (HS1) that is similar to but larger than in the atmosphere. Comparing the Brazil Margin results to published records from the North Atlantic, we are unable to account for the South Atlantic δ13C data with conservative mixing between northern and southern component water masses. Rapid input of abyssal water from the Southeast Atlantic could account for deglacial δ13C anomalies at the Brazil Margin but it would require a reversal in deep water flow direction compared to today. A new mid-depth water mass may explain similar HS1 δ13C values in both the North and South Atlantic, but contrasting oxygen isotopic values between the two basins do not support such a scenario. Instead, it appears that δ13C behaved non-conservatively during the deglaciation, possibly reflecting the input of carbon from an isotopically depleted source.