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Anthropogenic stressors pose substantial threats to the existence of coral reefs. Achieving successful coral recruitment stands as a bottleneck in reef restoration and hybrid reef engineering efforts. Here, we enhance coral settlement through the development of biomimetic microhabitats that replicate the chemical landscape of healthy reefs. We engineered a soft biomaterial, SNAP-X, comprising silica nanoparticles (NPs), biopolymers, and algal exometabolites, to enrich reef microhabitats with bioactive molecules from crustose coralline algae (CCA). Coral settlement was enhanced over 20-fold using SNAP-X-coated substrates compared with uncoated controls. SNAP-X is designed to release chemical signals slowly (>1 month) under natural seawater conditions, and can be rapidly applied to natural reef substrates via photopolymerization, facilitating the light-assisted 3D printing of microengineered habitats. We anticipate that these biomimetic chemical microhabitats will be widely used to augment coral settlement on degraded reefs and to support ecosystem processes on hybrid reefs.