Polyelectrolyte hollow capsules are versatile platforms typically used for encapsulation of a wide variety of macromolecules in their cavity. The polymer shell of these capsules as composed by alternating layers of oppositely charged polyelectrolytes also allows for adding additional functionalities. The properties of the shell can be for example engineered by trapping different nanoparticles in-between the shell layers and/or by attaching bioactive molecules such as antibodies to the outermost layer. Herein, iron oxide NPs were inmobilized into the shell of polyelectrolyte capsules and the outermost layer of the shell was covalently modified with anti peroxidase antibodies. These capsules act as prototype model system, aiming to obtain a microstructure with the potential capability to specifically recognize and separate macromolecules. Due to the magnetic nanoparticles in the capsule shell, the capsules together with the attached target might be extracted by magnetic field gradients. Here we verified this approach by extracting horseradish peroxidase from a solution through magnetic separation with capsules bearing antibodies against horseradish peroxidase. The bioactivity of the capsules and the high degree of specific antibody functionalization were confirmed and quantified through an enzymatic reaction mediated by the extracted horseradish peroxidase. (C) 2016 Elsevier Inc. All rights reserved.