In this work we have developed and implement a new approach for the study of magnetoliposomes using Monte Carlo simulations. Our model is based on interaction among nanoparticles considering magnetic dipolar, van der Waals, ionic-steric, and Zeeman interaction potentials. The ionic interaction between nanoparticles and the lipid bilayer is represented by an ionic repulsion electrical surface potential that depends on the nanoparticle-lipid bilayer distance and the concentration of ions in the solution. A direct comparison among transmission electron microscopy, vibrating sample magnetometer, dynamic light scattering, nanoparticle tracking analysis, and experimentally derived static magnetic birefringence and simulation data allow us to validate our implementation. Our simulations suggest that confinement plays an important role in aggregate formation.