Understanding how natural communities confront different types of natural and anthropogenic stressors has gained much more attention as global climate change imposes nearly unpredictable ecosystem states or regimes. In the Humboldt Current ecosystem this seems to be a priority task due to the complex dynamics caused by the El Niño Southern Oscillation (ENSO). Herein a 17-year (1991–2007) time-series data-set of macrobenthic community structure and environmental parameters from seasonal sampling from four fixed stations off Punta Coloso (23°45’S, 70°28’W northern of Chile) is analyzed. The aim of this study was to assess benthic responses to ENSO-associated anomalies. nMDS analysis revealed changes in community structure associated to El Niño (1997–1998) and La Niña (1999–2000). From 1991, communities gradually increased in dissimilarity up to 1998 but after 2000 dissimilarity decreased, thus approaching the early community structure in a counterclockwise like direction. This suggested a cyclical pattern throughout time, which was tested with a cyclicity analysis. The test showed a significant correlation between the dissimilarity biotic matrix and a perfect cyclicity model matrix. The finding of a 17-year cycle in the variation of community structure adds new insights and contrast to previous observations of increments in diversity and alternation of dominant taxa associated to environmental forcing. It needs to be revealed if this cycle forms part of a major decadal oscillation in the benthic subsystem. Nevertheless, this result is in line with the decadal pattern of variability observed for pelagic communities associated to warm and cold phases of ENSO.