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Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and electrochemical performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that in nanoporous carbons electrochemical oxidation of iodide forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide angle X-ray scattering (in situ SAXS/WAXS). In-situ Raman spectroscopy confirms the formation of triiodide and pentaiodide during iodide oxidation. Besides polyiodides, remarkable amounts of solid iodine are deposited in the carbon nanopores, as detected by in situ SAXS/WAXS. Combined with stochastic modelling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.