As ultra-high energy cosmic ray protons propagate through the universe, they undergo photo-meson interactions with the cosmic microwave background, generating the ‘cosmogenic’ neutrino flux. If, however, a substantial fraction of the cosmic ray primaries are heavy nuclei rather than protons, they would preferentially lose energy through photo-disintegration so the corresponding neutrino flux may be substantially depleted. We investigate this issue using a Monte Carlo simulation of cosmic ray propagation through intragalactic radiation fields and assess the impact of the altered neutrino fluxes on next-generation neutrino telescopes.