Abstract: While the low-energy excess observed at MiniBooNE remains unchallenged, it has become increasingly difficult to reconcile it with the results from other sterile neutrino searches and cosmology. Recently, it has been shown that non-minimal models with new particles in a hidden sector could provide a better fit to the data. As their main ingredients they require a GeV-scale kinetically mixed with the photon, and an unstable heavy neutrino with a mass in the 150 MeV range that mixes with the light neutrinos. In this letter we point out that atmospheric neutrino experiments (and, in particular, IceCube/DeepCore) could probe a significant fraction of the parameter space of such models by looking for an excess of “double-bang” events at low energies, as proposed in our previous work (Coloma et al., Phys Rev Lett 119(20):201804, 10.1103/PhysRevLett.119.20180, 2017). Such a search would probe exactly the same production and decay mechanisms required to explain the anomaly.