Atom probe tomography (APT) is a promising tool to measure the atomic-scale distribution of hydrogen in solid matter, which can be used to assess the hydrogen embrittlement susceptibility of materials. However, the accuracy of such measurements resulting from ambient charging and transfer experiments needs to be established. In this work, APT quantification of hydrogen (H) and deuterium (D) in a typical X65 pipeline steel has been determined after ambient charging and transfer to ascertain the contribution of artifacts to the measured H/D signal. A series of experimental workflows related to sample preparation (electropolishing, focussed ion beam) and electrochemical charging conditions (different electrolytes and charging potentials) were explored for H/D measurement using APT. The results show that APT can be used to measure charged H/D with statistical confidence after ambient charging and transfer, that hydrogen ingress occurs during electropolishing, and using a more negative charging potential will introduce more H/D into the material.