Liposomes encapsulating magnetic nanoparticles (MNPs), known as magnetoliposomes (MLs), have become a hot topic in biomedical research for applications in remote-triggered drug delivery and diagnostic imaging. One of the most crucial steps in the preparation of MLs is the purification of non-encapsulated MNPs, as a non-efficient purification can lead to misleading results. Purification is challenging especially when MNPs are loaded in the liposome lumen due to the small size differences between the MLs and the non-encapsulated MNPs. This work presents a comparison of three well known purification techniques, namely size exclusion chromatography, centrifugation and salt-induced aggregation, using five commercial MNPs with different configurations. The optimal purification techniques for two MNPs were studied further in the synthesis of MLs. In conclusion, we show that an efficient MLs purification requires the performance of a detailed study to select a valid method that is strongly dependent upon MNPs choices.