Reef benthic communities provide many important ecosystem functions such as nutrient cycling, carbonate accretion and tridimensional complexity. Yet, reefs worldwide face an uncertain future, being threatened by local and global impacts. As an alternative approach to evaluate communities’ changes, functional ecology aims to understand how species shape the environment and how functions conduct ecosystems’ dynamics. The aim of this study was to investigate the temporal dynamics (2013–2019) of the reef benthic community in the most pristine reef in Brazil, Rocas Atoll, using a functional diversity approach. We identified 48 organisms grouped into 17 functional entities (according to their traits’ combination), considering all sampling years. Benthic community was temporally dominated by functional entities responsible for providing low reef tridimensional complexity (represented mainly by turf algae). This dominance reflected in low values of functional entropy, due to uneven abundances distribution between unique functional entities, those that have unique trait combination. Functional richness oscillated over years, but did not show great changes in functional spaces, maintaining an equity in the number of functional entities and indicating stability of reef functions in Rocas Atoll, even with unequal abundances’ distribution. Our study is the first to use a functional approach in temporal scale and represents a baseline for South Atlantic, since it provides the actual state of reef benthic communities using a functional approach, in an environment with no direct anthropic impacts. This can help to predict the effects on some ecosystem functions caused by local and global changes and its consequence for ecosystem services.