Coral reef decline is an issue of concern around the globe. Remote and uninhabited coral areas are not exempt from facing changes in species composition and functionality due to global drivers. Quitasueño is a remote atoll within the Seaflower Biosphere Reserve, in the Southwestern Caribbean Sea. To evaluate the current status of the coral reefs in Quitasueño we sampled 120 stations through Rapid Ecological Assessment and evaluated four stations through Planar Point Intercept to compare the current percent cover of benthic groups with previous studies in the area. We found pronounced changes in coral and macroalgae covers in time, and great conspicuousness of multiple conditions of deterioration along Quitasueño, including diseases, coral predation, and aggression and invasion of coral colonies by macroalgae and sponges. The reef ecosystem seems to be facing a phase shift, in which the benthic cover previously dominated by hard corals is currently dominated by fleshy macroalgae. It is essential to evaluate the possible drivers of the extent of degradation of Quitasueño to understand the process of deterioration and mitigate the impacts.