The electronic structure of cobalt phthalocyanine (CoPc) changes upon encapsulation inside multi-walled carbon nanotubes (CoPc@MWNT), as detected in this research using Co-K-edge X-ray absorption near-edge structure spectroscopy (XANES) and Co-Kα1 resonant inelastic X-ray scattering (RIXS). The CoPc molecules are no longer planar once inside the nanotubes, and the molecular symmetry is found to change upon encapsulation from D4h to C4v symmetry. This change of symmetry increases the amount of p–d orbital mixing, which is seen in the spectra as a change in peak intensity. Energy shifts are also seen between CoPc and CoPc@MWNT, showing that Co in the encapsulated species is more oxidized due to electron donation from the phthalocyanine molecule to the surrounding nanotube. Trends seen in the spectra between CoPc and CoPc@MWNT can be calculated using density functional theory (DFT), which shows the molecular orbitals involved in different spectral features.