Background: Various techniques have been advocated for over half a century for the fabrication of transfer trays for indirect orthodontic bonding. Authors have aimed to provide better light curing and accuracy of bracket positioning to avoid bracket failure and get the best possible results. Aim: This study is aimed to compare bracket failure rate when transfer trays were fabricated with a glue gun material and polylactic acid (PLA) filament for an indirect bonding procedure. Materials and methods: Customized transfer trays were fabricated using a glue gun material and PLA filament, and an indirect bonding procedure was performed. Bracket failure was assessed at regular intervals with adhesive remnant index (ARI) scoring, and reasons for bracket failure were assessed. Results: Kolmogorov–Smirnov test was employed to test the normality of data. A Chi-square test was performed for the quantitative variables. Results showed higher bracket failure in the PLA transfer tray groups and in the mandibular arch, especially in the posterior region. Adhesive remnant index scores of 2 followed by 3 were prevalent, and the most common reason for bracket failure was an excessive force during PLA transfer tray retrieval followed by masticatory forces. Conclusions: Both the transfer tray methods are effective for an indirect bonding procedure. Polylactic acid transfer trays showed more bracket failure as compared to glue gun transfer trays, especially in the mandibular posterior region due to excessive force applied during tray retrieval. Clinical significance: This study aims to provide valuable information regarding the efficiency of various in-house methods of fabricating customized transfer trays and their effect on bracket failure rates.