Discovery of permanent magnetisation in molecules just like in hard magnets decades ago led to the proposal of utilising these molecules for information storage devices and also as Q‐bits in quantum computing. A significant breakthrough with a blocking temperature as high as 80 K has been recently reported for lanthanocene complexes. While enhancing the blocking temperature further remains one of the primary challenges, obtaining molecules that are suitable for the fabrication of the devices sets the bar very high in this area. Encouraged by the fact that our earlier predictions of potential single‐molecule magnets (SMMs) in lanthanide‐containing endohedral fullerenes have been verified, here we set out to undertake a comprehensive study on CoII‐ion‐encapsulated fullerene as potential SMMs. To study this class of molecules, we have utilised an array of theoretical methods ranging from density functional to ab initio CASSCF/NEVPT2 methods for obtaining reliable estimate of zero‐field splitting parameters D and E. Additionally, we have also employed, for the first time a combination of molecular dynamics based on DFT methods coupled with CASSCF/NEVPT2 methods to seek the role of conformational isomers in the relaxation of magnetisation. Particularly, we have studied, Co@C28, Co@C38 and Co@C48 cages and their isomers as potential target molecules that could yield substantial magnetic anisotropy. Our calculations categorically reveal a very large Ising anisotropy in this class of molecules, with Co@C48 cages predicted to yield D values as high as −127 cm−1. Our calculations on the smaller cages reveal the free movement of CoII ion inside the cage, leading to the likely scenario of faster relaxation of magnetisation. However, larger fullerene cages were found to solve this issue. Further models with incorporating units such as {CoOZn}, {CoScZnN} inside larger fullerenes yield axial zero‐field splitting values as high as −200 cm−1 with negligible E/D values. As these units represent a strong axiality coupled with a viable way to obtain air‐stable low‐coordinate CoII complexes, this opens up a new paradigm in the search of SMMs in this class of molecules.