Gold diffusion into silicon at room temperature was observed in real time with atomic resolution. Gold nanoclusters were formed on a silicon surface by an electrical discharge between a silicon tip and a gold coated tip inside an ultrahigh-vacuum transmission electron microscope (TEM) specimen chamber. At the moment of the gold nanocluster deposition, the gold nanoclusters had a crystalline structure. The crystalline structure gradually disappeared due to the interdiffusion between silicon and gold as observed after the deposition of gold nanoclusters. The shape of the nanocluster gradually changed due to the gold diffusion into the damaged silicon. The diffusion front between silicon and gold moved toward the silicon side. From the observations of the diffusion front, the gold diffusivity at room temperature was extracted. The extracted activation energy, 0.21 eV, matched the activation energy in bulk diffusion between damaged silicon and gold. This information is useful for optimizing the hybridization between solid-state and biological nanodevices in which gold is used as an adhesive layer between the two devices.