The present study aimed to investigate the impact of hardness from 3D printed transfer trays and dental crowding on bracket bonding accuracy. Lower models (no crowding group: Little's Irregularity Index (LII) < 3, crowding group: LII > 7, n = 10 per group) were selected at random, digitized, 3D printed, and utilized for semiautomated virtual positioning of brackets and tubes. Hard and soft transfer trays were fabricated with polyjet printing and digital light processing, respectively. Brackets and tubes were transferred to the 3D printed models and altogether digitized using intraoral scanning (IOS) and microcomputed tomography (micro-CT) for assessment of linear and angular deviations. Mean intra- and interrater reliability amounted to 0.67 +/- 0.34/0.79 +/- 0.16 for IOS, and 0.92 +/- 0.05/0.92 +/- 0.5 for the micro-CT measurements. Minor linear discrepancies were observed (median: 0.11 mm, Q1-Q3: -0.06-0.28 mm). Deviations in torque (median: 2.49 degrees, Q1-Q3: 1.27-4.03 degrees) were greater than angular ones (median: 1.81 degrees, Q1-Q3: 1.05 degrees-2.90 degrees), higher for hard (median: 2.49 degrees, Q1-Q3: 1.32-3.91 degrees) compared to soft (median: 1.77 degrees, Q1-Q3: 0.94-3.01 degrees) trays (p < 0.001), and torque errors were more pronounced at crowded front teeth (p < 0.05). In conclusion, the clinician should carefully consider the potential impact of hardness and crowding on bracket transfer accuracy, specifically in torque and angular orientation.