Although graphene looks attractive to replace indium tin oxide (ITO) in optoelectronic devices, the luminous efficiency of light emitting diodes (LEDs) with graphene transparent conducting electrodes has been limited by degradation in graphene taking place during device fabrication. In this study, it was found that the quality of graphene after the device fabrication was a critical factor affecting the performance of GaN-based LEDs. In this paper, the qualities of graphene after two different device fabrication processes were evaluated by Raman spectroscopy and atomic force microscopy. It was found that graphene was severely damaged and split into submicrometer-scale islands bounded by less conducting boundaries when graphene was transferred onto LED structures prior to the GaN etching process for p-contact formation. On the other hand, when graphene was transferred after the GaN etch and p-contact metallization, graphene remained intact and the resulting InGaN/GaN LEDs showed electrical and optical properties that were very close to those of LEDs with 200 nm thick ITO films. The forward-voltages and light output powers of LEDs were 3.03 V and 9.36 mW at an injection current of 20 mA, respectively.