The frequently underestimated effects of “in air” thermal treatment processing conditions such as temperature, duration, and heating and cooling rates in the design and efficiency of photoelectrodes fabricated for academic studies onto the most common commercial transparent conductive glass substrate i.e. fluorine-doped tin oxide (FTO) were investigated by X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, conductive atomic force microscopy, electrochemical impedance spectroscopy, and direct current and photoelectrochemical (PEC) measurements. The PEC response of Hematite photoanode thin films consisting of short nanorods thermally treated at 400 and 800°C upon fast or extended time conditions is inhibited by factors such as crystallinity, Sn diffusion, or substrate integrity. A “fast” thermal treatment in air at 750°C provided the best synergy between charge transfer resistance, Sn-diffusion from the FTO substrate, nanorod dimensions, reduced recombination, improved charge separation and minimized substrate damage. This study offers valuable fundamental and practical insights for a better understanding of the benefits and drawbacks of photoelectrode thermal processing, which is critical for the improvement of the PEC performance-reproducibility relationship for FTO-based solar water splitting systems and devices.