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Eu3+ and Tb3+ doped in nanocrystalline InBO3, GdBO3, and LaBO3 having three different morphs of calcite (CaCO3) such as Calcite, Vaterite, and Aragonite, respectively, were synthesized by glycine–nitrate combustion method. Luminescence due to Eu3+ and Tb3+ doped individually as well as simultaneously in these three different morphs of calcite were investigated and compared. Also the effect of concentration of dopant ions on the luminescence was studied. The highest photoluminescence emission intensity was observed for RE0.05M0.95BO3 (RE = Eu3+, Tb3+, M = In, Gd, La) samples. Further increase in doping led to concentration quenching of the luminescence. In case of the co-doped borates, the energy transfer between the co-doped rare earth ions was influenced by the host crystal structure. This study reveals that there is remarkable effect of the crystal structure of host and concentration of dopant ions on the luminescence.