there is an urgent need to overcome the limited reproducibility of this approach when scaling up the number of qubits and junctions. Fabrication methods based on subtractive patterning of superconductor–insulator–superconductor trilayers, used for more classical large-scale Josephson junction circuits, could provide the solution but they in turn often suffer from lossy dielectrics incompatible with high qubit coherence. In this work, we utilize native aluminum oxide as a sidewall passivation layer for junctions based on aluminum–aluminum-oxide–niobium trilayers, and use such junctions in qubits. We design the fabrication process such that the few-nanometer-thin native oxide is not exposed to oxide removal steps that could increase its defect density or hinder its ability to prevent shorting between the leads of the junction. With these junctions, we design and fabricate transmon-like qubits and measure time-averaged coherence times up to 30 μs at a qubit frequency of 5 GHz, corresponding to a qubit quality factor of one million. Our process uses subtractive patterning and optical lithography on wafer scale, enabling high throughput in patterning. This approach provides a scalable path toward fabrication of superconducting qubits on industry-standard platforms.