Molybdenum(II) complexes [MoX(CO)2(η3‐allyl)(CH3CN)2] (X = Cl or Br) were encapsulated in an aluminium‐pillared natural clay or a porous clay heterostructure and allowed to react with bidentate diimine ligands. All the materials obtained were characterised by several solid‐state techniques. Powder XRD, and 27Al and 29Si MAS NMR were used to investigate the integrity of the pillared clay during the modification treatments. 13C CP MAS NMR, FTIR, elemental analyses and low‐temperature nitrogen adsorption showed that the immobilisation of the precursor complexes was successful as well as the in situ ligand‐substitution reaction. The new complex [MoBr(CO)2(η3‐allyl)(2‐aminodipyridyl)] was characterised by single‐crystal X‐ray diffraction and spectroscopic techniques, and NMR studies were used to investigate its fluxional behaviour in solution. The prepared materials are active for the oxidation of cis‐cyclooctene using tert‐butyl hydroperoxide as oxidant, though the activity of the isolated complexes is higher. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)