The present work uses a multi-omics approach targeting the complexity and interconnection among the components modulating phenotypic plasticity in staghorn coral (Acropora cervicornis) clones subject to different depth conditions. Datasets describing gene expression, DNA methylation, microbial and symbiotic composition, and lipidome were developed for this project. Results were consistent with a multi-mechanism modulation of rapid acclimation in corals, underscoring the complexity of this process and the importance of a multifactorial approach to inform potential intervention to enhance coral adaptive capacity.