Metal deposition on self-assembled monolayers (SAMs) with different terminal organic functional groups is a growing area of research and the metal-organic interface has been extensively studied in the past two decades. Apart from impacting existing technologies, it may have a profound impact on the emerging future technologies such as molecular electronics. The morphology of the deposited metals is strongly influenced by the nature of the chemical interactions occurring at the interface of the organic functional group (OFG) of the SAM and the deposited metal. Our interest for such studies stems from different perspective, as we are interested in determining the impact of the interface on the morphology and hence the magnetic properties of the deposited magnetic materials. We have sputtered a magnetic material, permalloy (Ni79Fe21), on self-assembled monolayers of polar and nonpolar molecules, and have observed contrasting magnetic behaviors of permalloy on these surfaces. We have observed the formation of uniform film on polar regions and cluster are formed on nonpolar regions. Further investigations reveal that the cluster formation gives rise to superparamagnetism, while the uniform film shows a usual ferromagnetic behavior. The observed contrast in morphology and magnetism of Py is attributed to different growth mechanisms arising from difference in polarity of the SAM surfaces.