The study aims to evaluate the acoustic, thermal, and tribological performance of two geometrically identical harmonic gearboxes manufactured from Polylactic Acid (PLA) and Polyethylene Terephthalate Glycol (PETG) through Fused Filament Fabrication (FFF), with the objective of determining how material choice affects dynamic stability and long-term dimensional integrity. A custom experimental setup was developed to enable simultaneous, no-load endurance testing under controlled laboratory conditions, incorporating sound pressure level (SPL) measurements, thermal imaging, and high-resolution wear analysis of the Flexspline teeth. Each gearbox was subjected to ten cycles of 30-min operation, during which acoustic emissions and peak surface temperatures were recorded. Subsequently, a final wear analysis was conducted. The resulting dataset reveals material-dependent trends in both acoustic and thermal behaviour, with each polymer exhibiting distinct SPL evolution patterns and heat accumulation characteristics. Correlation between thermal rise and acoustic instability indicates that frictional processes at the tooth interface evolve differently for PLA and PETG over repeated cycling. Wear examination confirms significant geometric alterations and wear debris formation, consistent with the expected tribological degradation mechanisms in polymer–polymer contact. These findings underscore the significance of material selection in the design of additively manufactured harmonic drives, particularly for low-load, precision, and noise-sensitive applications, where subtle thermal and tribological effects can influence operational consistency and functional longevity.