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Organic spintronics has drawn the interest of the science community due to various applications in spin-valve devices. However, an efficient room-temperature Organic Spin Valve device has not been experimentally realized due to the complicated spin transport at the metal-organic interfaces. The present study focuses on a comprehensive understanding of the interfacial properties essential for advancing device performance and functionality. The structural and magnetic properties of the ultra-thin Cobalt (Co) films deposited on the fullerene (C60) layer are studied to investigate the origin of magnetic anisotropy in the metal-organic bilayer structures. Due to the mechanical softness of C60, penetration of ferromagnetic Co atoms inside the C60 film is confirmed by the X-ray reflectivity and Secondary Ion Mass Spectroscopy measurements. Grazing incidence small-angle X-ray scattering and atomic force microscopy provided information regarding the structural and morphological properties of the Co/C60 bilayers, angular dependent Magneto-optic Kerr effect measurements with varying Co layer thickness provided information about the growth-induced uniaxial magnetic anisotropy. In contrast to the inorganic silicon substrates, magnetic anisotropy in Co film tends to develop at 25 {\AA} thickness on the C60 layer, which further increases with the thickness of Cobalt. The anomalous behavior in coercivity and remanence variation along the nominal hard axis is explained by a two-grain Stoner-Wohlfarth model with intergranular exchange coupling. It is further confirmed by a non-uniform spatial distribution of magnetic domains investigated through Kerr microscopy. These anomalies could be attributed to the distribution of magneto-crystalline anisotropy and inhomogeneous strain caused by the formation of a diffused layer at the Co/C60 interface.