Structures made by scleractinian corals support diverse ocean ecosystems. Despite the importance of coral skeletons and their predicted vulnerability to climate change, few studies have examined the mechanical and crystallographic properties of coral skeletons at the micro- and nano-scales. Here, we investigated the interplay of crystallographic and microarchitectural organization with mechanical anisotropy within Porites skeletons by measuring Young’s modulus and hardness along surfaces transverse and longitudinal to the primary coral growth direction. We observed micro-scale anisotropy, where the transverse surface had greater Young’s modulus and hardness by ∼ 6 GPa and 0.2 GPa, respectively. Electron backscatter diffraction (EBSD) revealed that this surface also had a higher percentage of crystals oriented with the a-axis between ± 30–60∘, relative to the longitudinal surface, and a broader grain size distribution. Within a region containing a sharp microscale gradient in Young’s modulus, nanoscale indentation mapping, energy dispersive spectroscopy (EDS), EBSD, and Raman crystallography were performed. A correlative trend showed higher Young’s modulus and hardness in regions with individual crystal bases (c-axis) facing upward, and in crystal fibers relative to centers of calcification. These relationships highlight the difference in mechanical properties between scales (i.e. crystals, crystal bundles, grains). Observations of crystal orientation and mechanical properties suggest that anisotropy is driven by microscale organization and crystal packing rather than intrinsic crystal anisotropy. In comparison with previous observations of nanoscale isotropy in corals, our results illustrate the role of hierarchical architecture in coral skeletons and the influence of biotic and abiotic factors on mechanical properties at different scales. Statement of significanceCoral biomineralization and the ability of corals’ skeletal structure to withstand biotic and abiotic forces underpins the success of reef ecosystems. At the microscale, we show increased skeletal stiffness and hardness perpendicular to the coral growth direction. By comparing nano- and micro-scale indentation results, we also reveal an effect of hierarchical architecture on the mechanical properties of coral skeletons and hypothesize that crystal packing and orientation result in microscale anisotropy. In contrast to previous findings, we demonstrate that mechanical and crystallographic properties of coral skeletons can vary between surface planes, within surface planes, and at different analytical scales. These results improve our understanding of biomineralization and the effects of scale and direction on how biomineral structures respond to environmental stimuli.