We study the modification of the detected flavor content of ultra high-energy astrophysical neutrinos in the presence of non-standard interactions of neutrinos with the Earth matter. Unlike the case of new physics affecting the propagation from the source to the Earth, non-standard Earth matter effects induce a dependence of the flavor content on the arrival direction of the neutrino. We find that, within the current limits on non-standard neutrino interaction parameters, large deviations from the standard 3ν oscillation predictions can be expected, in particular for fluxes dominated by one flavor at the source. Conversely they do not give sizable corrections to the expectation of equalized flavors in the Earth for sources dominated by production via pion-muon decay-chain.