Understanding how coral holobionts, including microbial and algal symbionts, contribute to stress resilience is critical for safeguarding reef ecosystems under accelerating environmental change. This study investigated the genetic and microbiome determinants of stress recovery in the reef-building coral Acropora kenti. Five host genotypes were exposed to different resource environments, and post-stress resilience was assessed using storage lipid recovery as a physiological indicator. To characterize microbial, we generated bacterial 16S rRNA amplicon profiles across all genotypes and treatments at four timepoints. Bacterial community composition was strongly correlated with functional lipid profiles, suggesting indirect microbiome-mediated effects on stress recovery. Both bacterial and algal symbiont assemblages were shaped by host genotype, leading to substantial within-population variability in recovery potential. These sequencing datasets provide a resource for examining the interactions among coral host metabolites, microbial community structure, and environmental factors, and support strategies such as genotype selection and microbiome manipulation for enhancing coral resilience.