Hydrogen fuel cells currently rely on expensive platinum group metal nanoparticle catalysts [1]. For green hydrogen production and utilization to become widely commercially viable, the cost of the devices that produce and utilize hydrogen must be significantly reduced. Platinum group metal-free (PGM-free) catalysts have the potential to greatly reduce this cost, and materials consisting of single transition metal atoms embedded in a nitrogen-doped graphitic carbon structure have shown particular promise for use as fuel cell cathodes [2]. A better understanding of the active site properties in these materials is still needed, however, to improve their stability and design new active site structures with enhanced properties [3]. Due to the atomic-scale nature of the active sites in these materials, scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS) have proven invaluable for demonstrating their atomically dispersed nature and composition [4]. Conventional STEM techniques have limited ability to correlate the local bonding environment and oxidation state of the metal atoms, for example, or track changes in the catalyst structure both during synthesis and as a result of cycling, which would provide a deeper understanding of the relationship between active site and catalyst properties.Here, we demonstrate advanced electron microscopy techniques that provide both enhanced and previously inaccessible information about PGM-free catalysts and their active sites. We show developments in automated identification of metal atom positions, which we use both to generate statistics about interatomic distances and to automatically position the STEM probe on individual atoms for EELS data acquisition. The former allows information about the presence of dual-metal site structures to be extracted, for example, and the latter allows compositional information with improved SNR to be obtained. Rapid automatic probe positioning also presents the opportunity for measuring the effect of local bonding environment on metal atom oxidation state, which cannot be obtained manually since these sites are typically unstable under the beam. In addition, we will show identical-location STEM (IL-STEM) techniques that allow the evolution of catalyst morphology and properties to be tracked at high resolution across synthesis steps and accelerated stress tests [5]. In particular, we use IL-STEM imaging and EELS to track deposition of graphitic material on the surface of a PGM-free catalyst that significantly improves the material’s durability, as well as track the change in the nanoscale graphitic carbon structure of the material as a function of electrochemical cycling. By providing access to enhanced compositional and bonding state information, as well as the ability to track properties as a material evolves, these techniques will advance our knowledge of PGM-free catalysts and enable better control over their properties in the future, accelerating wide-spread use of hydrogen fuel cells [6].