Caribbean reefs have suffered decline in coral cover in recent decades due to recurrent anthropogenic and natural stressors. The regional collapse of the sea urchin Diadema antillarum, combined with overfishing, has contributed to a phase-shift of coral reef communities towards fleshy macroalgal dominance. Here, we examine the population dynamics of D. antillarum at five sites in Puerto Rico from 2011 to 2016 and determine trends between the sea urchin and local benthic habitats. The sea urchin population exhibited low but stable densities (with slight, but non-significant trend of increase), yet showed variability between sites. Large urchins (>60 mm test diam.) were the most abundant across sites and through time, followed by medium urchins (41–60 mm test diam.), whereas small individuals (<40 mm) were rare, indicating recruitment-limitation. Spatial and temporal differences in benthic habitats were not related to local D. antillarum abundances. Macroalgae cover declined at all sites over the 6 years, ranging 5–86%, whereas live coral cover also decreased across all sites (ranging 4–38%). Diadema antillarum populations in Puerto Rico appear stable with limited evidence for recovery trends back to pre-mass mortality densities. Full population recovery may take longer than expected; however, evidence indicates that the contemporary low-density D. antillarum population represents a novel stable regime.