A novel approach for the direct synthetic diamond–GaN integration via deposition of the high-quality nanocrystalline diamond films directly on GaN substrates at temperatures as low as 450–500 °C is reported. The low deposition temperature allows one to avoid degradation of the GaN quality, which is essential for electronic applications The specially tuned growth conditions resulted in the large crystalline diamond grain size of 100–200 nm without coarsening. Using the transient “hot disk” measurements it is demonstrated that the effective thermal conductivity of the resulting diamond/GaN composite wafers is higher than that of the original GaN substrates at elevated temperatures. The thermal crossover point is reached at ≈95–125 °C depending on the thickness of the deposited films. The developed deposition technique and obtained thermal characterization data can lead to a new method of thermal management of the high power GaN electronic and optoelectronic devices.