We report on a novel fabrication of nanostructures of silver (Ag) germanium telluride (GeTe) at room temperature and the control of resistive switching using them. We systematically fabricated Ag seed nanoparticles of various sizes by thermal annealing and demonstrated that deposition of GeTe by RF sputtering onto the Ag seed nanoparticles spontaneously produced nanostructures including broccoli-like, hollow nanostructures comprised predominantly of nanocrystalline grains of Ag, Ag3Ge, Ag2Te, and Ag5Te3. The nanostructure shape and the constituent crystalline phases depend on the amount of Ag used for the seeds. The nanostructure formation followed nanoscale phase separation and crystallization into an unexpected phase from the phase diagram, including a metastable state. The structural changes were characteristic of the Ag nanoparticles; no significant structural changes occurred for GeTe deposition onto Ag films. As an application of the spontaneously formed nanostructures, we demonstrated a control resistive switching when a voltage was applied with a lateral Ag electrode pair deposited onto the top. We found that the Ag amount used for the seed formation determined the polarity of resistive switching and the SET/RESET voltages. By increasing the Ag amount, the resistive switching turned from the clockwise direction to the counter-clockwise direction, and the SET/RESET voltages were lowered.