For portable, remotely operated systems in space and defense, relaxed vacuum requirements are a strong advantage of ion trap mass analyzers. However, ion traps are believed to have insufficient capability for isotope ratio measurement because they fundamentally restrict sampling capacity. Focusing on modifications to the detection sequence of a digitally driven three-dimensional quadrupole ion trap, operating in resonance ejection mode, we investigated the improved performance for isotope ratio precision and accuracy. Due to xenon's inert nature and wide span of isotopes, xenon isotope ratios provide an excellent marker of processes (e.g., radioactive decay and planetary atmospheric escape) that would be ideally measured by in situ mass spectrometry. To target xenon isotope ratio analyses specifically, we implemented data acquisition system modifications for enhanced y-axis resolution measurements and signal filtering. In this manner, we show measurement precision improvements from ∼±100 to ∼±0.1 ‰ and accuracy improvements from ∼30 to ∼0.5 ‰ for our targeted isotopes of interest.