Operando synchrotron-based Fourier transform infrared (SR-μFTIR) microspectroscopy takes advantage of the high brilliance of synchrotron radiation to collect high-quality spectra with a superior signal-to-noise ratio (S/N) in subsecond timeframes. This technique achieves a spatial resolution finer than ten micrometers, enabling real-time operando mapping of electrode surfaces during battery operation, even under high C rate. The combination of both high temporal and spatial resolution makes (SR-μFTIR) a powerful tool for investigating dynamic electrochemical processes at the microscale. Operando SR-μFTIR microspectroscopy can be applied to the study of electrode materials, electrolytes, and electrode–electrolyte interfaces. It is especially valuable for the elucidation of reaction mechanisms taking place in noncrystalline and/or lightweight element-based electrodes, such as organic electrode materials. Herein, we show how a simple modification of the commercially available ECC-Opto-Std (ELCELL) cell allows unraveling the potential of operando SR-μFTIR microspectroscopy for investigating organic electrodes. This setup is applied to study the reaction mechanism of polyimide derived from 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) in lithium, sodium, and calcium cells. During the charge/discharge process of the polyimide, a reversible change in the carbonyl bands intensities is observed with the concomitant appearance of two main new bands. Density functional theory calculations assign these bands to competing enolation/carbonylation processes with direct interactions between the aromatic ring and alkaline metal ions present in the electrolyte. Furthermore, the enhanced spectral resolution of synchrotron radiation provides a more detailed insight into the stepwise mechanism pathway in Na cells, as well as rate-dependent variations in the reaction mechanism.