While neutrino physics enters precision era, several important unknowns remain. Atmospheric neutrinos allow to simultaneously test key oscillation parameters, with Super-Kamiokande experiment playing a central role. We discuss results from atmospheric neutrino oscillation analysis of the full dataset from Super-Kamiokande I-IV phases. Further, we discuss tests of non-standard neutrino interactions with atmospheric neutrinos in Super-Kamiokande.