We combined advanced TEM (HRTEM, HAADF, EELS) with solid-state (SS)MAS NMR and electroanalytical techniques (GITT, etc.) to understand the site-specific sodiation of selenium (Se) encapsulated in a nanoporous carbon host. The architecture employed is representative of a wide number of electrochemically stable and rate-capable Se-based sodium metal battery (SMB) cathodes. SSNMR demonstrates that during the first sodiation, the Se chains are progressively cut to form an amorphous mixture of polyselenides of varying lengths, with no evidence for discrete phase transitions during sodiation. It also shows that Se nearest the carbon pore surface is sodiated first, leading to the formation of a core–shell compositional profile. HRTEM indicates that the vast majority of the pore-confined Se is amorphous, with the only localized presence of nanocrystalline equilibrium Na2Se2 (hcp) and Na2Se (fcc). A nanoscale fracture of terminally sodiated Na–Se is observed by HAADF, with SSNMR, indicating a physical separation of some Se from the carbon host after the first cycle. GITT reveals a 3-fold increase in Na+ diffusivity at cycle 2, which may be explained by the creation of extra interfaces. These combined findings highlight the complex phenomenology of electrochemical phase transformations in nanoconfined materials, which may profoundly differ from their “free” counterparts.