The coral holobiont forms the foundation of reef ecosystems and its study is crucial for understanding coral resilience to anthropogenic climate change. Over a five-week period, coral nubbins were exposed to ambient and thermal stress conditions, with meta-transcriptome and metabolite data generated from each sample. This study overlapped with a mass spawning event of Montipora capitata, therefore providing insights into the general coral stress phenome as well as the impacts on thermal stress on reproduction.