AbstractNon-equilibrium quasiparticles are possible sources for decoherence in superconducting qubits because they can lead to energy decay or dephasing upon tunneling across Josephson junctions (JJs). Here, we investigate the impact of the intrinsic properties of two-dimensional transmon qubits on quasiparticle tunneling (QPT) and discuss how we can use quasiparticle dynamics to gain critical information about the quality of JJ barrier. We find the tunneling rate of the non-equilibrium quasiparticles to be sensitive to the choice of the shunting capacitor material and their geometry in qubits. In some devices, we observe an anomalous temperature dependence of the QPT rate below 100 mK that deviates from a constant background associated with non-equilibrium quasiparticles. We speculate that this behavior is caused by high transmission sites/defects within the oxide barriers of the JJs, leading to spatially localized subgap states. We model this by assuming that such defects generate regions with a smaller effective gap. Our results present a unique in situ characterization tool to assess the uniformity of tunnel barriers in qubit junctions and shed light on how quasiparticles can interact with various elements of the qubit circuit.