Nickel-rich cathodes provide improved specific capacity, which leads to higher gravimetric energy density, which, in turn, is critical for electric vehicles. However, poor long-term capacity retention at elevated temperatures/high C rates (the rate of charge and discharge on a battery) stems from material issues: surface phase changes, corrosive side reactions with the electrolyte, ion dissolution, and propagation of cracks. Introducing dopants, developing nanoscale surface coatings, and graded core–shell structures all improved the electrochemical performance of nickel-rich cathodes. However, material-level understanding of the effect of Li composition and distribution in Ni-rich cathodes is limited due to a lack of characterization methods available that can directly image Li at the nanoscale. Hence, it is critical to establish methods such as atom probe tomography (APT) that have both nanometer-scale spatial resolution and high compositional sensitivity to quantitatively analyze battery cathodes. To fully realize its potential as a method for quantitative compositional analysis of commercial Li-ion batteries, we provide a comprehensive description of the challenges in sample preparation and analyze the dependency of the analysis parameters, specifically laser pulse energy on the measured stoichiometry of elements in a high-Ni-content cathode material LiNi0.8Co0.15Al0.05O2 (NCA). Our findings show that the stoichiometry variations cannot be explained by charge–state ratios or Ga implantation damage alone during FIB preparation, indicating that additional factors such as crystallographic orientation may need to be considered to achieve quantitative nanoscale compositional analysis of such battery cathodes using APT.