During geomagnetic storms the flux of radiation belt electrons can increase, decrease, or stay constant, depending on the competition between acceleration and loss mechanisms. We focus on loss of relativistic electrons. We use low-altitude polar-orbiting spacecraft and analyze fluxes of tens to hundreds of keV protons and relativistic (>1.5 MeV) electrons during a moderate geomagnetic storm, with a long-lasting recovery phase (4–5 d). Using data from four local times, we find that the loss of relativistic electrons is confined within the anisotropic proton zone and that a spatially limited loss of relativistic electrons is spatially collocated with increased loss of protons. The proton pitch angle distributions within these peaks are consistent with moderate to strong pitch angle scattering due to electromagnetic ion cyclotron (EMIC) waves. The loss of relativistic electrons collocated with protons is found at all four local times considered (0300, 0700, 1400, 1700 MLT). Since anisotropic proton distributions can under certain conditions generate EMIC waves, we find strong indications that the observed relativistic electrons are scattered into the atmospheric loss cone by EMIC waves. EMIC wave scattering is less efficient at high equatorial pitch angles but very efficient near the loss cone, thereby controlling the loss rate of relativistic electrons to the atmosphere. Our observations in and near the loss cone support theoretical work suggesting that EMIC waves can cause scattering loss to the atmosphere of relativistic electrons over the course of a geomagnetic storm.