It is being increasingly recognized that small coral reef fishes are highly specialised on branching coral substrata and are threatened by reef degradation. In the past, it has been assumed that medium-sized mobile coral reef fishes may be less at risk. This assumes medium-sized mobile fishes are not as equally associated with and susceptible to the loss of live coral, especially early in their ontogeny. Here we use observations of habitat use and compositional analysis to show that three mobile medium-sized fishes, Siganus vulpinus (Siganidae), Zebrasoma scopas (Acanthuridae) and Heniochus varius (Chaetodontidae), are associated with live coral substrata early in ontogeny and less so as adults on coral reefs in Kimbe Bay, Papua New Guinea. Small size classes of S. vulpinus and Z. scopas showed a preference toward using branching and bushy live coral, as well as structurally intact dead coral, suggesting an underlying importance of reef structural complexity during early life stages. H. varius was associated with foliose and plate coral through all size classes, but selectivity declined as sub-adults and adults. In general, all species became more generalist in their use of reef substrata at larger sizes, but S. vulpinus and Z. scopas tended to avoid open and less structurally complex reef habitats, such as, sand, soft corals and sponges, while H. varius avoided dead coral substrata. Our results confirm that juvenile stages may be a critical bottleneck that exposes medium-sized reef fishes to the same risks small reef fish species experience due to declining coral cover.