Synchrotron radiation X-ray diffraction (XRD) with nanoscale beam size was used here for in situ and in operando study of micro-supercapacitors (MSC) with gel electrolyte and MXene Ti3C2Tx electrodes. The electrode structure was characterized as a function of applied voltage and distance from the gap separating electrodes using microscopic cells with cylindrical shape designed for transmission mode XRD. The devices with gel electrolytes based on H2SO4 (with H2O/PVA and DMSO/PVA) showed stable performance with no changes in MXene structure under voltage swaps between positive and negative values. Experiments with KI-based electrolytes demonstrated changes of MXene structure correlated with decrease of energy storage parameters under conditions of increased operation voltage starting from 0.8 V. The optimal performance of the MSCs was observed when the MXene structure remained unchanged upon switching the applied voltage polarity. The changes of inter-layer distance of MXene upon swap of applied voltage correlate with decrease of device performance and are undesirable for stable operation of MSC's. We also tested feasibility of X-ray fluorescence (XRF) for characterization of electrolyte ion migration in MSCs using 2D element mapping. Irreversible sorption of iodine by MXene was found using XRF mapping of charged electrodes using standard in-plane MSC device and KI electrolyte.