The construction of artificial structures, such as seawalls, is increasing globally, resulting in loss of habitat complexity and native species biodiversity. There is increasing interest in mitigating this biodiversity loss by adding topographic habitat to these structures, and/or seeding them with habitat-forming species. Settlement tile experiments, comparing colonisation of species to more and less complex habitats, have been used to inform eco-engineering interventions prior to their large-scale implementation. Most studies have focused on applying one type of intervention (either adding habitat structure or seeding with native organisms), so it is unclear whether there are greater benefits to biodiversity when multiple interventions are combined. Using a fully orthogonal experiment, we assessed the independent and interactive effects of habitat structure (flat vs. crevice/ridges) and seeding with native oysters (unseeded vs. seeded) on the biodiversity of four different functional groups (sessile and mobile taxa, cryptobenthic and pelagic fishes). Concrete tiles (flat unseeded, flat seeded, complex unseeded and complex seeded) were deployed at two sites in Sydney Harbour and monitored over 12 months, for the survival and colonisation of oysters and the species density and abundances of the four functional groups. The survival of seeded oysters was greater on the complex than flat tiles, at one of the two sites, due to the protective role of crevices. Despite this, after 12 months, the species density of sessile invertebrates and the percentage cover of seeded and colonising oysters did not differ between complex and seeded tiles each of which supported more of these variables than the flat unseeded tiles. In contrast, the species density of mobile invertebrates and cryptobenthic fishes and the MaxN of pelagic fishes, at 1 month, were only positively influenced by seeding with oysters, which provided food as well as habitat. Within the complex seeded and unseeded tiles, there was a greater species density of sessile taxa, survival and percentage cover of oysters in the crevices, which were more humid and darker at month 12, had lower high temperature extremes at months 1 and 12, than on the ridges or flat tiles. Our results suggest that eco-engineering projects which seek to maximise the biodiversity of multiple functional groups on seawalls, should apply a variety of different microhabitats and habitat-forming species, to alter the environmental conditions available to organisms.