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Abstract In scenarios with large extra dimensions (LEDs), the fundamental Planck scale can be low enough that collisions between high-energy particles may produce microscopic black holes. High-energy cosmic neutrinos can carry energies much larger than a PeV, opening the door to a higher energy range than Earth-based colliders. Here, for the first time, we identify a number of unique signatures of microscopic black holes as they would appear in the next generation of large-scale neutrino observatories such as IceCube-Gen2 and the Pacific Ocean Neutrino Explorer. These signatures include new event topologies, energy distributions, and unusual ratios of hadronic-to-electronic energy deposition, visible through Cherenkov light echos due to delayed neutron recombination. We find that the next generation of neutrino telescopes can probe LEDs with a Planck scale up to 6 TeV, though the identification of unique topologies could push their reach even further.