Climate warming and associated sea ice reductions in Antarctica have modified habitat conditions for some species. These include the congeneric Adélie, chinstrap and gentoo penguins, which now demonstrate remarkable population responses to regional warming. However, inconsistencies in the direction of population changes between species at different study sites complicate the understanding of causal processes. Here, we show that at the South Orkney Islands where the three species breed sympatrically, the less ice-adapted gentoo penguins increased significantly in numbers over the last 26 years, whereas chinstrap and Adélie penguins both declined. These trends occurred in parallel with regional long-term warming and significant reduction in sea ice extent. Periodical warm events, with teleconnections to the tropical Pacific, caused cycles in sea ice leading to reduced prey biomass, and simultaneous interannual population decreases in the three penguin species. With the loss of sea ice, Adélie penguins were less buffered against the environment, their numbers fluctuated greatly and their population response was strong and linear. Chinstrap penguins, considered to be better adapted to ice-free conditions, were affected by discrete events of locally increased ice cover, but showed less variable, nonlinear responses to sea ice loss. Gentoo penguins were temporarily affected by negative anomalies in regional sea ice, but persistent sea ice reductions were likely to increase their available niche, which is likely to be substantially segregated from that of their more abundant congeners. Thus, the regional consequences of global climate perturbations on the sea ice phenology affect the marine ecosystem, with repercussions for penguin food supply and competition for resources. Ultimately, variability in penguin populations with warming reflects the local balance between penguin adaptation to ice conditions and trophic-mediated changes cascading from global climate forcing.