The Antarctic Peninsula (AP) is one of the three places on Earth that registered the most intense warming in the last 50 years, almost five times the global mean. This warming has strongly affected the cryosphere, causing the largest ice-shelf collapses ever observed and the retreat of 87% of glaciers. Ecosystem responses, although increasingly predicted, have been mainly reported for pelagic systems. However, and despite most Antarctic species being benthic, responses in the Antarctic benthos have been detected in only a few species, and major effects at assemblage 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. 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 runoff, 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 (for example, of tolerable sedimentation) and alternative equilibrium states, depending on the reversibility of the changes, could be possible traits of 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.