The Super-Kamiokande experiment has played a major role in astrophysics by investigating low energy O(10)~MeV neutrinos. It has notably been instrumental in characterizing the 8B solar neutrino spectrum and currently exhibits the best sensitivity to relic neutrinos from distant supernovae. Fully realizing the potential of low energy astrophysical searches however requires significantly reducing backgrounds from cosmic muon spallation. Here, I present an in-depth study of spallation backgrounds, in particular of the showers produced by muons passing through the detector. This study, and in particular the implementation of new FLUKA-based simulations, are expected to significantly impact analysis strategies for a wide variety of low energy searches in Super-Kamiokande.