Coral nurseries and associated techniques are the most common and widespread reef restoration methods worldwide. Due to the rapid decline of coral reefs, coral nurseries need to be eco-friendlier and adapted for effective upscaling to support large restoration projects. We suggest new design and fabrication processes associated with coral gardening and transplantation with 3D printing technology to offer a beneficial solution for growing coral fragments in on-land and underwater nurseries. We describe multiple combinations of building nurseries through the integration of biomimetic substrates and novel solutions for attaching coral fragments. Our methods are supported with supplemental testing of two hybrid substrate designs and coral mounting structures, building upon previous studies in the Gulf of Eilat/Aqaba (GoE/A), Red Sea. We identified and quantified marine invertebrates colonizing the surfaces of our substrates with environmental DNA (eDNA) by targeting the mitochondrial COI gene. We evaluated our coral fragments with and without our mounting structures to obtain an indication of total protein as a proxy for tissue health. We demonstrate the ability to design hybrid nurseries with custom mounting structures using biomimetic substrates, such as large ceramic artificial reefs, or with an interlocking mesh for holding numerous fragments to maximize out-planting efforts. We propose several methods for both land and underwater nurseries catered to various restoration initiatives for cost-effective up-scaling to meet the demands of global reef restoration.