Community composition is one of the main factors influencing the ecological functioning of any given ecosystem, with a more diverse community providing a larger set of services. Benthic community composition can vary at spatial and temporal scales, with the dynamics of primary production and benthic food availability being key determinants of community structure of a given system. Studies have indicated shifts in benthic community composition at sub-Antarctic Islands over a period of 30 years, linked to variability in food availability driven by climate change. Here, we aim to evaluate possible short-term variability in benthic community composition at the sub-Antarctic archipelago Prince Edward Islands (PEIs), sampling stations across three hydrographically dynamic regions over two consecutive years, 2016–2017. The results indicated significantly higher species richness and abundance in 2017 than in 2016, with some taxa also showing variation among regions around the PEIs. Such effects can be linked to different substratum type or hydrographic regime. This study further contributes to understanding variability and changes in benthic communities in the near future, an essential information to develop efficient management strategies for this vulnerable marine system.