Restored oyster reefs support diverse communities of motile benthic organisms (small fishes and macroinvertebrates). These communities represent a critical component of estuarine food webs and frequently include juveniles of ecologically and economically important species that utilize oyster reefs as nurseries. Oyster-related metrics are commonly used to quantify restoration success, yet it is also important to examine communities of oyster-associated organisms when attempting to identify ecological convergence between natural and restored oyster reefs. Here, we compare the community composition of motile benthic organisms over time at one restored and three natural oyster (Crassostrea virginica) reefs in the Loxahatchee River estuary (Florida, USA) as one means of assessing restoration success. We also examine the effects of vertical relief on motile benthic organisms following restoration. The community of motile benthic organisms at the 1.93-ha restoration reef gradually began to resemble natural communities in the months following reef construction. Within ~22 months, biomass and community composition were similar between natural and restored habitats. At that point, the mean biomass of motile benthic organisms at the restoration site had reached 83.6 g/m2(versus 89.8 g/m2at nearby natural reefs), and the restored reef supported >1600 kg of small, motile, oyster-associated organisms. Biomass values increased more rapidly in high-relief sections of the restored reef (30 cm vs. 15 cm reef height), particularly during the first year following restoration. High-relief areas were also characterized by increased oyster densities, greater oyster-generated rugosity, and decreased sedimentation. Our findings suggest that small differences in reef design can have important implications for restoration success as well as food web structure and dynamics via shifts in community composition.