In this paper we study nonstandard neutrino interactions as an example of physics beyond the standard model using atmospheric neutrino data collected during the Super-Kamiokande I (1996–2001) and II (2003–2005) periods. We focus on flavor-changing-neutral-currents (FCNC), which allow neutrino flavor transitions via neutral current interactions, and effects which violate lepton nonuniversality and give rise to different neutral-current interaction-amplitudes for different neutrino flavors. We obtain a limit on the FCNC coupling parameter, , at 90% C.L. and various constraints on other FCNC parameters as a function of the nonuniversality coupling, . We find no evidence of nonstandard neutrino interactions in the Super-Kamiokande atmospheric data.