Stoichiometric rare-earth materials have demonstrated extremely narrow inhomogeneous photoluminescence-excitation linewidths because the rare-earth cations occupy uniform crystallographic sites. These narrow linewidths make them strong candidates for quantum information storage by providing access to transitions with extremely long coherence times on the order of hours. Determining the chemical origins of defects that may broaden linewidths and reduce performance is an important step toward exploiting stoichiometric systems’ advantages. Here, we present EuAl3(BO3)4 as a system for defect-performance correlation studies since it can be grown as optically transparent single crystals and has a large Eu–Eu separation. Large crystals grown from two flux systems incorporate percent-level substitutions of flux cations. Additionally, the material’s three polytypic modifications, including the newly detailed C2/c space group polymorph, can coexist within single crystals. The sharply divided polymorph domains are revealed by photoluminescence mapping. Polymorph domains are also present in EuAl3(BO3)4 samples produced flux-free by microwave-assisted sintering in only 45 min. We anticipate that these mapping studies will be a crucial step in the quest to identify local heterogeneity (substitutions, polymorphs, strain, etc.) in the next generation of quantum information storage materials.