GeV-TeV gamma-ray and PeV-EeV neutrino backgrounds provide a unique window on the nature of the ultra-high-energy cosmic-rays (UHECRs). We discuss the implications of the recent Fermi-LAT data regarding the extragalactic gamma-ray background (EGB) and related estimates of the contribution of point sources as well as IceCube neutrino data on the origin of the UHECRs. We calculate the diffuse flux of cosmogenic $\gamma$-rays and neutrinos produced during the UHECRs propagation and derive constraints on the possible cosmological evolution of UHECR sources. In particular, we show that the mixed-composition scenario which is in agreement with both (i) Auger measurements of the energy spectrum and composition up to the highest energies and (ii) the ankle-like feature in the light component detected by KASCADE-Grande, is compatible with both the Fermi-LAT measurements and with current IceCube limits.