Numerous studies have addressed the excellent properties of Ce-doped YAG crystals for utilization in lighting applications. However, the differences in the photoluminescence and defect formation of YAG crystals obtained by different methods have not been elucidated. In this study, the effects of the crystallization path of YAG: Ce on the local structure of its emission site and defect formation were investigated. Ce-doped YAG crystal were prepared in three ways: (1) solid-state reaction, (2) heat-treatment of YAG glass, and (3) crystallization from a supercooled YAG melt by a controlled cooling process with deep supercooling state. A shift in the photoluminescence peak of 3 nm and a significant enhancement in the thermoluminescence was observed in the sample obtained by the crystallization of a supercooled melt. As the intensity of thermoluminescence has been associated with the defects formed, positron annihilation lifetime spectroscopy was performed to investigate the defects. All crystallized samples exhibited two components of positron lifetime, and both these components increased in the sample.