Optimized conditions for imaging and spectroscopic/elemental mapping of thin perfluorosulfonic acid (PFSA) ionomer layers in fuel cell electrodes by scanning transmission electron microscopy (STEM) have been investigated. The proper conditions were first identified using model systems of either Nafion ionomer-coated nanostructured thin film catalysts or thin films on nanoporous Si. These analysis conditions were then applied in a quantitative study of the ionomer through-layer loading for two differently-prepared electrode catalyst layers using electron energy loss (EELS) and energy dispersive X-ray spectroscopy (EDS) in the STEM. The electron-beam induced damage to the PFSA ionomer was quantified by following the fluorine mass loss with electron dose/exposure and was mitigated by several orders of magnitude using cryogenic specimen cooling and a higher incident electron voltage. Multivariate statistical analysis was applied to the analysis of both EELS and EDS spectrum images for data de-noising and unbiased separation of the independent components related to the catalyst, ionomer, and support distributions within the catalyst layers.