Coastal substratum topography shapes microhabitat conditions both directly, by modulating abiotic environmental factors, and indirectly, by influencing the establishment of topography-associated biota. Consequently, structural differences between natural rocky shores and modern engineered coastal infrastructure are expected to alter microhabitat formation in urban seascapes, by reshaping interactions between topography, abiotic conditions, and biogenic habitat structure. Here, we tracked the development of microclimate conditions (temperature, light, humidity) across 12 months on three eco-engineered panel designs installed on an intertidal seawall. Abiotic factors were assessed at both the panel scale, and at the scale of specific topographic features (outer surfaces, plateaus, overhangs, crevices). Effects of biological colonisation (i.e., canopy cover) were disentangled from direct topographic effects by assessing bare, temporarily installed reference panels at each timepoint. Structurally complex panels exhibited lower mean temperatures, and a greater range of light and humidity conditions than flat panels. Inner topographic features, such as crevices and overhangs, reduced temperatures and light intensities, and increased humidity compared to outer surfaces. Macroalgal canopy formation further reduced most temperature and light parameters, while elevating humidity. These effects occurred irrespective of topography; however, complex panels exhibited cumulative topographic-biogenic effects that created unique microenvironmental conditions not found on flat, colonized panels. Our findings provide quantitative, mechanistic insights into how engineered habitat complexity drives fine-scale microclimate patterns, with practical applications for designing multifunctional, ecologically sustainable coastal infrastructure. Restoring (micro-)habitat conditions on anthropogenically modified shorelines through biomimicry and nature-based solutions is key to enhancing habitat suitability and climate change resilience in urbanized environments.