The diffusion behavior of Mg in Mg/N co-implanted GaN is investigated in response to a set of annealing conditions and methodologies, namely, 1000 °C/30 min thermal anneal, by high-temperature pulsed gyrotron microwave annealing at 1420 or 1500 °C, or by thermal and microwave annealing, sequentially. After 1000 °C annealing, the diffusion of Mg in GaN is found to be negligible, as measured by secondary ion mass spectrometry. Annealing by gyrotron microwave annealing alone induces the diffusion of Mg at a rate on the order of 10−12 cm2/s. However, the use of a thermal anneal before microwave gyrotron annealing reduces this rate by an order of magnitude to 10−13 cm2/s. We find that a model that considers Mg diffusion from an inhomogeneous medium that contains a defect-rich implanted region near-surface to a relatively pristine region below the implant range better explains the observed diffusion behavior than a conventional model that assumes a homogeneous medium. By analyzing the diffusion behavior using the Boltzmann–Matano method, we present a discussion of reduction in [VGa] by thermal annealing at 1000 °C, leading to a suppressed diffusion coefficient during subsequent high-temperature annealing relative to diffusion after 1420/1500 °C annealing alone. This effect holds potential for improvement in the precision of selectively doped regions for future applications based on the (Al)GaN material system. An improved field profile control in real devices can increase the breakdown and current-handling capabilities in power electronic applications.