Objective: This study aims to investigate the transfer accuracy of two different design versions for 3D-printed indirect bonding (IDB) trays. Materials and Methods: Digital plaster models of 27 patients virtually received vestibular attachments on every tooth using OnyxCeph³™ (Image Instruments, Chemnitz, Germany). Based on these simulated bracket and tube positions, two versions of transfer trays were designed for each dental arch and patient, which differed in the mechanism of bracket retention: Variant one (V1) had arm-like structures protruding from the tray base and reaching into the horizontal and vertical bracket slots, and variant two (V2) had a pocket-shaped design enclosing the brackets from three sides. Both tray designs were 3D-printed with the same digital light processing (DLP) printer using a flexible resin-based material (IMPRIMO® LC IBT/Asiga MAX™, SCHEU-DENTAL, Iserlohn, Germany). Brackets and tubes (discovery® smart/pearl, Ortho-Cast M-Series, Dentaurum, Ispringen, Germany) were inserted into the respective retention mechanism of the trays and IDB was performed on corresponding plaster models. An intraoral scan (TRIOS® 3W, 3Shape, Copenhagen, Denmark) was performed to capture the actual attachment positions and compared to the virtually planned positions with Geomagic© Control (3D Systems Inc., Rock Hill, SC, USA) using a scripted calculation tool, which superimposed the respective tooth surfaces. The resulting attachment deviations were determined in three linear (mesiodistal, vertical and orovestibular) and three angular (torque, rotation and tip) directions and analyzed with a descriptive statistical analysis. A comparison between the two IDB tray designs was conducted using a mixed model analysis (IBM, SPSS® Statistics 27, Armonk, NY, USA). Results: Both design versions of the 3D-printed IDB trays did not differ significantly in their transfer accuracy (p > 0.05). In total, 98% (V1) and 98.5% (V2) of the linear deviations were within the clinically acceptable range of ±0.2 mm. For the angular deviations, 84.9% (V1) and 86.8% (V2) were within the range of ±1°. With V1, most deviations occurred in the mesiodistal direction (3.3%) and in rotation (18%). With V2, most deviations occurred in the vertical direction (3.8%) and in palatinal and lingual crown torque (16.3%). Conclusions: The transfer accuracies of the investigated design versions for 3D-printed IDB trays show good and comparable results albeit their different retention mechanisms for the attachments and are, therefore, both suitable for clinical practice.