Niobium coaxial cavities with internal quality factors exceeding <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mn>1.4</mml:mn> <mml:mo>×</mml:mo> <mml:msup> <mml:mn>10</mml:mn> <mml:mn>9</mml:mn> </mml:msup> </mml:ma

Group-V materials such as niobium and tantalum have become popular choices for extending the performance of circuit quantum electrodynamics (cQED) platforms, allowing for quantum processors and memories with reduced error rates and more modes. The complex surface chemistry of niobium, however, makes identifying the main modes of decoherence difficult at millikelvin temperatures and single-photon powers. We use niobium coaxial quarter-wave cavities to study the impact of etch chemistry, prolonged atmospheric exposure, and the significance of cavity conditions prior to and during cooldown---in particular, niobium hydride evolution---on single-photon coherence. We demonstrate cavities with quality factors ${Q}_{\mathrm{int}}\ensuremath{\gtrsim}1.4\ifmmode\times\else\texttimes\fi{}{10}^{9}$ in the single-photon regime, a 15-fold improvement over aluminum cavities of the same geometry. We rigorously quantify the sensitivity of our fabrication process to various loss mechanisms and demonstrate a two- to fourfold reduction in the two-level system loss tangent and a three- to fivefold improvement in the residual resistance over traditional buffered chemical polishing etching techniques. Finally, we demonstrate transmon integration and coherent cavity control while maintaining a cavity coherence of 11.3 ms. The accessibility of our method, which can be easily replicated in academic laboratory settings, together with the demonstration of its performance, mark an advancement in three-dimensional cQED.