This study aimed to elucidate factors limiting power conversion efficiency (PCE) in GaN-based micro-light-emitting diodes (μ-LEDs). To this end, we investigated the effects of operating temperature and chip-size of μ-LEDs on their efficiency. For the investigation, 460 nm-emitting μ-LEDs with various chip-sizes were fabricated; then their characteristics were carefully measured from 100 to 400 K. As the chip-size decreases and the operating temperature increases, their PCE and external quantum efficiency (EQE) decrease, while voltage efficiency (VE) increases. This indicates that the EQE plays a more important role than the VE in determining the PCE of μ-LEDs. Particularly, for a chip-size of 20 × 20 μm², the EQE was very lower and the ideality factor was unexpectedly higher compared to the others for all operating temperatures, which is believed to be due to the critical plasma damage at the sidewall during dry-etching process for the chip-size < 20 × 20 μm².