Growth anomalies (GAs) impact both coral skeleton and soft tissues and are detrimental to reef health. This tumor-like disease is increasingly found throughout the tropics and is commonly associated with high human population density, yet little is known about the etiology, pathology, or calcification behavior of the disease. Here, we investigate potential mechanisms involved in the development of GAs through chemical and morphological characterization of GA skeletons in Porites compressa from a site of high disease prevalence (Coconut Island, Hawaii). A comprehensive suite of trace elements and boron isotopes (δ11B) were measured in skeletal GAs to assess calcification behavior and uptake of essential and toxic metals. Scanning electron microscopy of GA skeleton revealed it to be highly porous consisting of a matrix with a disorganized crystal structure, in contrast to the dense well-organized normal skeleton of P. compressa. Elemental analyses revealed decreased Mg/Ca and increased U/Ca in GA skeletons relative to paired unaffected samples, suggesting a decreased abundance of rapidly accreting microstructures “centers of calcification” in the GAs. Estimates of carbonate system parameters based on δ11B and B/Ca measurements indicate reduced pH (–0.05 units) and [CO32–] within the calcifying fluid of GAs, which may have implications for GA calcification. Higher levels of essential (V/Ca and Mo/Ca) elements in GAs potentially indicate increased abundance of holobiont-associated, nitrogen-fixing bacteria and higher Sb/Ca and Nd/Ca indicate alteration in the accumulation/depuration of these toxic metals. In aggregate, our findings show that dystrophic calcification processes could explain structural differences seen in GA vs unaffected skeletons and highlight the use of approaches herein to shed light on disease pathophysiology in corals.