Magnetic memory systems are one of the recently strongly investigated topics in the research area of spintronics. Amongst the different data storage systems, magnetic nanoparticles are of high interest since they can often store large amounts of data on small scales. Such magnetic nanoparticles, however, pose new challenges, such as oxidation and agglomeration. Here, we show micromagnetic simulations using MagPar, which solves the Landau–Lifshitz–Gilbert equation using finite elements, to analyze the energy density of iron nano-spheres. For spheres of 10 nm or 25 nm and different oxide shell thicknesses, 3D energy maps were calculated. Interestingly, the cubic magneto-crystalline anisotropy led to a non-uniform energy distribution of the magnetic nano-spheres, with the number of extrema decreasing for larger oxide layer thicknesses. In the case of the agglomeration of four nano-spheres, the distances between the nano-spheres strongly modified the system’s magnetic properties, where an oxide shell enabled bringing the nano-spheres closer together before they start influencing each other, which was evaluated by comparing the magnetic properties of these agglomerates with the single nano-spheres. For the oxide coated system, the maximum packing density could be increased by about 12%, as compared to the non-coated system, indicating that a higher data density can be reached by preparing a matrix of magnetic nano-spheres with oxide shells.