Researchers, tourism operators, and reef stakeholders have joined forces along the Great Barrier Reef (GBR) in a collaborative effort under the Coral Nurture Program (CNP) to enhance natural recovery of high-value reef sites through targeted coral propagation and out-planting. However, as stressors threaten the longevity and success of reef restoration outcomes there is a growing need to strategically select corals based on traits such as thermal tolerance. Therefore, we evaluate the efficacy of strategic stock selection using a novel Multi-Taxa Phenotyping system to determine whether “winners” (e.g., thermally tolerant corals) can successfully be identified in situ and if the process of propagation and outplanting impacts thermal performance in the long term. We tracked phenotyped corals on the native reef and in coral nurseries over 18months (through a mass bleaching event) to cross reference real-world performance under stress and during recovery against predicted performance. Results indicate that the phenotyping system can successfully separate top and bottom performers within and between species and sites. Further similar stress responses were observed across nursery fragments and reef colonies indicating that thermal performance rankings are not impacted during propagation.