Southern Ocean ecosystems matter for us all because they are important in Earth System processes and contribute to food security; they are also undergoing some of the most rapid changes being seen anywhere on the planet. The changes are not uniform, with warming in some regions and cooling in others, and the ecological effects being observed in these areas also vary. These changes need to be interpreted in the context of historical changes generated by harvesting of marine mammals, fish and Antarctic krill at various times over the last two centuries. To examine the relative importance of the factors that determine ecosystem structure and functioning requires integrated analyses of whole ecosystem operation from ‘end-to-end’ (microbes to whales and from small (<10 km) to circumpolar scales). We present a perspective that highlights the urgent need for concerted action, and that analyses of Southern Ocean ecosystems have relevance for analyses of ecosystems across the global ocean.