Unraveling ion conduction limitations in nanothin ionomer films is crucial for designing efficient ionomer−catalyst interfaces and improving redox efficiency in electrochemical devices. This work took a multifaceted approach to understand local proton conduction environments in sub-μm thick films of three fluorocarbon-based ionomers, Nafion, 3M PFSA and 3M PFIA with IEC ∼ 0.91, 1.21, and 1.61 mequiv/g, respectively. After incorporating fluorescent photoacid probe pyranine (HPTS) into films, the extent of proton conduction (I d /I p ), local proton concentration, pH, and ionic domain size (d id ) were predicted by monitoring the ratio of fluorescence intensity of deprotonated (I d ) to that of the protonated (I p ) state of HPTS. I d /I p decreased with film thickness and followed the trend: 3M PFIA > 3M PFSA > Nafion. A higher water uptake did not necessarily lead to higher I d /I p indicating that other factors than water uptake control proton conduction under confinement. Size of the ionic domains (d id ), measured independently using in-plane reflection small-angle X-ray scattering and fluorescence spectroscopy, followed the same trend as I d /I p . As the RH and film thickness decreased, d id became smaller. The close match of d id obtained from both techniques supported the reliability of information confered by fluorescence spectroscopy about key controlling parameters of the local proton conduction environment. The highest I d /I p of 3M PFIA films was attributed to its flexible, multiacidic side chain that helped to form larger ionic domains with better phase segregation. Conversely, smaller, extremely acidic and poorly phase segregated ionic domains with highly confined water molecules led to lower I d /I p in Nafion films, despite high water uptake.