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The study of the effects of high-energy particle irradiation on trilayer Josephson junctions has allowed us to investigate the influence of defects and interfacial intermixing on the junction electrical characteristics. In this paper, we investigated the influence of 2-MeV helium ion irradiation with doses up to 5.25 × 1016/cm2 on the tunneling behavior of Nb/Al-AlOx/Nb Josephson junctions. The modeling of the irradiation-induced chemical changes, combined with transmission-electron-microscopy characterization, indicates that over 2 nm of atomic intermixing occurs at all interfaces. Surprisingly, the quality of the tunneling characteristics is not significantly degraded, although some properties were affected: 1) The onset of the quasi-particle current characteristic of the electrodes' sum gap, Δ1 + Δ2, decreased from 2.8 to 2.6 mV; 2) the temperature onset of the Josephson current dropped from 9.2 K to 9.0 K; and 3) the normal resistance, Rn, increased by <; ~ 20%. The dependence of the Josephson current on the magnetic field was not significantly altered. Modeling using proximity theory indicated that the irradiation-induced changes in the current-voltage (I -V) characteristics are likely due to an increased drop in the order parameter near the barrier interface as a result of a reduced mean free path in the Al proximity layer from Nb and O contamination.