Underwater visual surveys of coral reefs are the primary method managers use to monitor coral health. However, these surveys are limited to visual signs, such as bleaching and tissue loss lesions, which occur only after significant stress has accumulated. More holistic characterization of coral health can allow for better monitoring of reef changes across natural environmental gradients, in response to anthropogenic stress and after disturbance events (e.g. disease outbreaks, mass bleaching, dredging, run-off events). Various methods exist to evaluate the health of the coral holobiont that do not depend on visual signs, including histological assessment, microbiome dysbiosis and metabolic profiles, yet these tools are rarely deployed concurrently. We present a clear, readily deployable protocol for sampling and preserving coral fragments, including (a) extraction of coral metabolites for analysis, (b) preservation of microbiome DNA for sequencing and (c) preservation of coral tissues for histopathology. Combined with visual surveys, these methods provide an unparalleled, holistic characterization of coral health. We provide a field-tested, optimized protocol for conducting coral sampling. This protocol guides the user through concurrent assessments of coral tissue structure and the holobiont microbiome and metabolome, and directs the user to useful resources for downstream data analysis. This protocol facilitates quantitative characterization of coral health beyond visual surveys alone, which is a valuable step forward in reef research and management and will improve our ability to describe, model and mediate impacts to coral reefs.