The Antarctic Peninsula (AP) is one of three places on Earth that registered the most intense warming in the last 50 years, almost five times the global mean. The cryosphere was rapidly affected registering the largest ice-shelves collapses ever observed and 87 % of glaciers in retreat. Ecosystem responses, although increasingly predicted, have been mainly reported for pelagic systems. However, and despite that most Antarctic species being benthic, registered responses in the Antarctic benthos were restricted to few species and major effects at community level are unknown. This is probably due to the scarcity of baselines against which to assess change. We performed repeat surveys of coastal benthos in 1994, 1998 and 2010 analyzing community structure and environmental variables at King George Island, Antarctica. Here we report a marked shift in an Antarctic benthic community that can be linked to ongoing climate change. However, rather than temperature as the primary factor, we highlight the resulting increased sediment run-off, triggered by glacier retreat as the potential causal factor. The sudden shift from a “filter feeders-ascidian domination” to a “mixed assemblage” suggests that thresholds (e.g. of tolerable sedimentation) and alternative equilibrium states, depending on the reversibility of the changes, could be possible traits in this ecosystem. Sedimentation processes will be increasing under the current scenario of glacier retreat and attention needs to be paid to its effects along the AP.