The biomineralization of bone remains a puzzle. During Haversian remodeling in the dense human cortical bone, osteoclasts excavate a tunnel that is then filled in by osteoblasts with layers of bone of varying fibril orientations, resulting in a lamellar motif. Such bone represents an excellent possibility to increase our understanding of bone as a material as well as bone biomineralization by studying spatio/temporal variations in the biomineral across an osteon. To this end, fluorescence computed tomography and diffraction scattering computed tomography with sub-micrometer resolution is applied to obtain position resolved fluorescence spectra and diffraction patterns in a 3D volume. The microstructural properties of the apatite biomineral are not homogeneous but depend critically on the time point at which it was laid down. This indicates that the nature of bone biomineral is highly dependent on the microenvironment during bone formation and remodeling.