The inclusion compounds formed between β-cyclodextrin (β-CD) and the tetrafluoroborate salts [Cp‘Mo(η4-C6H8)(CO)2][BF4] and the neutral derivatives Cp‘Mo(η3-C6H7)(CO)2 [Cp‘ = Cp (η5-C5H5), Ind (η5-C9H7)] were studied by means of elemental analysis, FTIR spectroscopy, thermogravimetric analysis (TGA), powder X-ray diffraction (XRD), and magic-angle spinning (MAS) NMR (13C, 11B). Additional information concerning the possible structure of the inclusion compounds was obtained from ab initio calculations using a two-layer approximation. The cationic and neutral η5-cyclopentadienyl analogues form stable two-to-one (host-to-guest) channel-type inclusion compounds in a crystalline state. By contrast, the η5-indenyl analogues form only weak complexes with β-CD and it is evident that the organometallic guests are easily liberated from the host cavities. The ab initio calculations revealed that the steric hindrance arising from the presence of the indenyl ligand is a possible explanation for the experimentally observed lower stability of these compounds.