Magnetized liposome (magnetosomes) labels can overcome diffusion limitations in bioassays through fast and easy magnetic attraction. Our aim therefore was to advance the understanding of factors influencing their synthesis focusing on encapsulation strategies and synthesis parameters. Magnetosome synthesis is governed by the surface chemistry and the size of the magnetic nanoparticles used. We therefore studied the two possible magnetic labelling strategies, which are the incorporation of small, hydrophobic magnetic nanoparticles (MNPs) into the bilayer core (b-liposomes) and the entrapment of larger hydrophilic MNPs into the liposomes' inner cavity (i-liposomes). Furthermore, they were optimized and compared for application in a DNA bioassay. The major obstacles observed for each of these strategies were on the one hand the need for highly concentrated hydrophilic MNPs, which is limited by their colloidal stability and costs, and on the other hand the balancing of magnetic strength vs. size for the hydrophobic MNPs. In the end, both strategies yielded magnetosomes with good performance, which improved the limit of detection of a non-magnetic DNA hybridization assay by a factor of 3-8-fold. Here, i-liposomes with a magnetization yield of 5% could be further improved through a simple magnetic pre-concentration step and provided in the end an 8-fold improvement of the limit of detection compared with non-magnetic conditions. In the case of b-liposomes, Janus-like particles were generated during the synthesis and yielded a fraction of 15% magnetosomes directly. Surprisingly, further magnetic pre-concentration did not improve their bioassay performance. It is thus assumed that magnetosomes pull normal liposomes through the magnetic field towards the surface and the presence of more magnetosomes is not needed. The overall stability of magnetosomes during storage and magnetic action, their superior bioassay performance, and their adaptability towards size and surface chemistry of MNPs makes them highly valuable signal enhancers in bioanalysis and potential tools for bioseparations. Graphical abstract.