The charging of nanoporous carbon via electrodeposition of solid iodine from iodide-based electrolyte is an efficient and ecofriendly method to produce battery cathodes. Here, the interactions at the carbon/iodine interface from first contact with the aqueous electrolyte to the electrochemical polarization conditions in a hybrid cell are investigated by a combination of in situ and ex situ methods. EQCM investigations confirm the flushing out of water from the pores during iodine formation at the positive electrode. XPS of the carbon surface shows irreversible oxidation at the initial electrolyte immersion and to a larger extent during the first few charge/discharge cycles. This leads to the creation of functional groups at the surface while further reactive sites are consumed by iodine, causing a kind of passivation during a stable cycling regime. Two sources of carbon electrode structural modifications during iodine formation in the nanopores have been revealed by in situ Raman spectroscopy, (i) charge transfer and (ii) mechanical strain, both causing reversible changes and thus preventing performance deterioration during the long-term cycling of energy storage devices that use iodine-charged carbon electrodes.