This study investigates the reuse of mussel shell waste as a secondary raw material in bio-cement mortars designed for the additive manufacturing of artificial reefs for marine habitat restoration. The novelty of the research lies in combining a high recycled shell content (60 wt.%), low-clinker cement, and two 3D-printing techniques: Extruded Material Systems (EMS) and Powder-Based Systems (PBS). Mechanical performance was evaluated through flexural and compressive tests after 7, 28, and 91 days under both air and freshwater curing conditions, while environmental impacts were assessed through Life Cycle Assessment (LCA). The LCA evaluated both the environmental performance of shell-based mixtures compared with conventional materials and the impacts associated with the investigated fabrication techniques. The best-performing bio-mixtures achieved compressive strengths up to 46.01 MPa and flexural strengths up to 9.91 MPa after freshwater curing, demonstrating the suitability of shell-based mortars for submerged applications. LCA results showed reduced impacts in land use and mineral resource depletion compared with conventional mixtures, despite slightly higher energy and water demands associated with shell pre-treatment. The results demonstrate the technical and environmental feasibility of integrating aquaculture waste into sustainable 3D-printed marine restoration solutions.