Urbanization is leading to biodiversity loss through habitat homogenization. The smooth, featureless surfaces of many marine urban structures support ecological communities, often of lower biodiversity, distinct from the complex natural habitats they replace. Eco-engineering (design for ecological co-benefits) seeks to enhance biodiversity and ecological functions on urban structures. We assessed the benefits to biodiversity of retrofitting four types of complex habitat panels to an intertidal seawall at patch (versus flat control panels) and site (versus unmodified control seawalls and reference rocky shores) scales. Two years after installation, patch-scale effects of complex panels on biodiversity ranged from neutral to positive, depending on the protective features they provided, though all but one design (honeycomb) supported unique species. Water-retaining features (rockpools) and crevices, which provided moisture retention and cooling, increased biodiversity and supported algae and invertebrates otherwise absent. At the site scale, biodiversity benefits ranged from neutral at the high- and mid-intertidal to positive at the low-intertidal elevation. The results highlight the importance of matching eco-engineering interventions to the niche of target species, and environmental conditions. While species richness was greatest on rockpool and crevice panels, the unique species supported by other panel designs highlights that to maximize biodiversity, habitat heterogeneity is essential.