Despite the importance of marine megafauna on ecosystem functioning, their contribution to the oceanic carbon cycle is still poorly known. Here, we explored the role of baleen whales in the biological carbon pump across the southern hemisphere based on the historical and forecasted abundance of five baleen whale species. We modelled whale-mediated carbon sequestration through the sinking of their carcasses after natural death. We provide the first temporal dynamics of this carbon pump from 1890 to 2100, considering both the effects of exploitation and climate change on whale populations. We reveal that at their pre-exploitation abundance, the five species of southern whales could sequester 4.0 × 10 5 tonnes of carbon per year (tC yr −1 ). This estimate dropped to 0.6 × 10 5 tC yr −1 by 1972 following commercial whaling. However, with the projected restoration of whale populations under a RCP8.5 climate scenario, the sequestration would reach 1.7 × 10 5 tC yr −1 by 2100, while without climate change, recovered whale populations could sequester nearly twice as much (3.2 × 10 5 tC yr −1 ) by 2100. This highlights the persistence of whaling damages on whale populations and associated services as well as the predicted harmful impacts of climate change on whale ecosystem services.