Iron biomineralisation is critical for life. Nature capitalises on the physical attributes of iron biominerals for a variety of functional, structural and sensory applications. Although magnetism is an integral property of iron biominerals, the role it plays in their nano-assembly remains a fundamental, unanswered question. This is well exemplified by the magnetite-bearing radula of chitons. Chitons, a class of marine mollusc, create the hardest biomineral of any animal in their abrasion-resistant, self-sharpening teeth4. Despite this system being subjected to a range of high resolution imaging studies, the mechanisms that drive mineral assembly remain unresolved. However, the advent of quantum imaging technology provides a new avenue to probe magnetic structures directly. Here we use quantum magnetic microscopy, based on nitrogen-vacancy centres in diamond, to attain the first subcellular magnetic profiling of a eukaryotic system. Using complementary magnetic imaging protocols, we spatially map the principal mineral phases (ferrihydrite and magnetite) in the developing teeth of Acanthopleura hirtosa with submicron resolution. The images reveal previously undiscovered long-range magnetic order, established at the onset of magnetite mineralisation. This is in contrast to electron microscopy studies that show no strong common crystallographic orientation. The quantum-based magnetic profiling techniques presented in this work have broad application in biology, earth science, chemistry and materials engineering and can be applied across the range of systems for which iron is vital.