Cobalt (11) phthalocyanine (CoPc) molecules have been encapsulated within the supercage of zeolite-Y. The square-planar complex, being larger than the almost spherical cage, is forced to adopt a distorted geometry on encapsulation. A comparative spectroscopic and magnetic investigation of CoPc encapsulated in zeolite-Y and in the unencapsulated state is reported. These results supported by molecular modeling have been used to understand the nature and extent of the loss of planarity of CoPc on encapsulation. The encapsulated molecule is shown to be the trans-diprotonated species in which the center of inversion is lost due to distortions required to accommodate the square complex within the zeolite. Encapsulation also leads to an enhancement of the magnetic moment of the CoPc. This is shown to be a consequence of the nonplanar geometry of the encapsulated molecule resulting in an excited high-spin state being thermally accessible.