In this research we present the novel technology that was developed using low-cost materials and 3D printing to allow for in operando nanoscale investigations of perfluorosulfonic acid membranes under vanadium oxygen fuel cell (VOFC) and direct methanol fuel cell (DMFC) conditions, using conductive atomic force microscopy. We detail the process of designing, iterating, fabricating, and validating our novel 3D printed imaging cell. The justifications for the design choices are explained in detail. Heating and relative humidity control are added to the cell as additional features for more accurate environmental simulation. Using the cell, we image Nafion membranes under VOFC conditions and compare our findings with previous research. We found that thinner membranes show higher current densities than thicker membranes. Furthermore, under VOFC conditions we observe the same shrinking behavior observed in previous research as the ionic strength of electrolytes that Nafion is exposed to increases. We imaged Nafion membranes under DMFC conditions and found that the operating temperature and anode catalysts play an important role in observing nanoscale proton conductivity. Finally, we detail the process of synthesizing low-valency vanadium/sulfuric acid electrolytes and end with an investigation into VO/TiO2 catalysts using density functional theory. This investigation helps to explain the atomic processes occurring on a model catalyst system that can catalyze the oxidative dehydrogenation of methanol to formaldehyde.