Long persistence phosphors are promising materials for energy-saving applications, due to their ability to temporarily store and release light. While boron is known to dramatically extend the afterglow persistence to longer than 8 h in strontium aluminates, previous attempts to understand the role of boron neglected any nanoscale-related effects and have been inconclusive. Herein, nanoscale-resolved cathodoluminescence mapping is correlated with selected area electron diffraction and with energy dispersive x-ray spectroscopy analysis using a 2 angstrom-diameter probe. The salient aspect of this unique approach is that one can not only determine the elemental distribution in the phosphor microstructure, but more importantly, one can discriminate between the distributions of different divalent and trivalent luminescing ions. We demonstrate that the extremely long afterglow is due to the boron dopant via two key roles: ( 1) facilitating dominance of the long persistence phase during the microstructural evolution and ( 2) promoting more uniform distribution of the optically active, Eu2+ ion in the Sr2+ cation sublattice.