Particles in a yet unexplored dark sector with sufficiently large mass and small gauge coupling may form purely gravitational atoms (quantum gravitational bound states) with a rich phenomenology. In particular, we investigate the possibility of having an observable signal of gravitational waves or ultrahigh-energy cosmic rays from the decay of gravitational atoms. We show that, if ordinary Einstein gravity holds up to the Planck scale, then within the Lambda-cold dark matter model (ΛCDM), the frequency of the gravitational wave signal produced by the decays is always higher than 1013 Hz. An observable signal of gravitational waves with smaller frequency from such decays, in addition to probing near Planckian dark physics, would also imply a departure from Einstein gravity near the Planck scale or an early epoch of nonstandard cosmology. As an example, we consider an early universe cosmology with a matter-dominated phase, violating our assumption that the Universe is radiation dominated after reheating, which gives a signal in an interesting frequency range for near-Planckian bound states. We also show how gravitational atoms arise in the minimal Planckian interacting dark matter scenario and compute their gravitational wave signature.