Astrophysical neutrinos are powerful tools for investigating the fundamental properties of particle physics through their flavor content. In this Letter, we perform the first general new physics study on ultrahigh energy neutrino flavor content by introducing effective operators. We find that, at the current limits on these operators, new physics terms cause maximal effects on the flavor content; however, the flavor content on the Earth is confined to a region related to the assumed initial flavor content. Furthermore, we conclude that a precise measure of the flavor content on the Earth will provide orders of magnitude improvement on new physics bounds. Finally, we discuss the current best fits of flavor content of the IceCube data and their interplay with new physics scenarios.