Coral reefs rely upon the highly optimized coral–Symbiodiniaceae symbiosis, making them sensitive to environmental change and susceptible to anthropogenic stress. Coral bleaching is predominantly attributed to photo-oxidative stress, yet nutrient availability and metabolism underpin the stability of symbioses. Recent studies link symbiont proliferation under nutrient enrichment to bleaching; however, the interactions between nutrients and symbiotic stability are nuanced. Here, we demonstrate how bleaching is regulated by the forms and ratios of available nutrients and their impacts on autotrophic carbon metabolism, rather than algal symbiont growth. By extension, historical nutrient conditions mediate host–symbiont compatibility and bleaching tolerance over proximate and evolutionary timescales. Renewed investigations into the coral nutrient metabolism will be required to truly elucidate the cellular mechanisms leading to coral bleaching.