The magnetic release of catalytically active enzymes from vesicular compartments within aggregated nanomaterials has been demonstrated. These nanomaterials, magnetic nanoparticle-vesicle aggregates (MNPVs), were formed by the self-assembly of biotinylated silica-coated Fe3O4 nanoparticles, biotinylated vesicles and tetrameric avidin. The unique features of nanoscale magnetite allow adhesion between membranes to be combined with magnetically triggered transit of reagents across membranes. Adding short spacers between the adhesive biotin groups and the nanoparticle or vesicle surfaces was found to strengthen binding to avidin, with binding of avidin to biotinylated bilayers and biotinylated nanoparticles monitored by quartz crystal microgravimetry with dissipation (QCM-D). Three different reagents were released from the vesicle compartments of MNPVs by a pulse of alternating magnetic field, with the release of a dye modelling the release of small molecule substrates, and the release of cytochrome c modelling the release of biological polymers, such as enzymes. To confirm that enzymes could be released and maintain activity, trypsin was encapsulated and shown to digest casein after magnetically triggered release.