  The performance of superconducting qubits is often limited by dissipation and
two-level systems (TLS) losses. The dominant sources of these losses are
believed to originate from amorphous materials and defects at interfaces and
surfaces, likely as a result of fabrication processes or ambient exposure.
Here, we explore a novel wet chemical surface treatment at the Josephson
junction-substrate and the substrate-air interfaces by replacing a buffered
oxide etch (BOE) cleaning process with one that uses hydrofluoric acid followed
by aqueous ammonium fluoride. We show that the ammonium fluoride etch process
results in a statistically significant improvement in median $\text{T}_1$ by
$\sim22\%$ ($p=0.002$), and a reduction in the number of strongly-coupled TLS
in the tunable frequency range. Microwave resonator measurements on samples
treated with the ammonium fluoride etch prior to niobium deposition also show
$\sim33\%$ lower TLS-induced loss tangent compared to the BOE treated samples.
As the chemical treatment primarily modifies the Josephson junction-substrate
interface and substrate-air interface, we perform targeted chemical and
structural characterizations to examine materials' differences at these
interfaces and identify multiple microscopic changes that could contribute to
decreased TLS.
