Coral calcification is a complex biologically controlled process of hard skeleton formation, and it is influenced by environmental conditions. The chemical composition of coral skeletons responds to calcification conditions and can be used to gain insights into both the control asserted by the organism and the environment. Boron and its isotopic composition have been of particular interest because of links to carbon chemistry and pH. In this study, we acquired high-resolution boron images (concentration and isotopes) in a skeleton sample of the azooxanthellate cold-water coral Lophelia pertusa. We observed high boron variability at a small spatial scale related to skeletal structure. This implies differences in calcification control during different stages of skeleton formation. Our data point to bicarbonate active transport as a critical pathway during early skeletal growth, and the variable activity rates explain the majority of the observed boron systematic. Coral skeletal high-resolution boron systematics can shed new light on a still enigmatic control of coral calcification.