In this contribution we report a synthetic strategy for the encapsulation of functional biomolecules within MOF-based microcapsules. We employ an agarose hydrogel droplet Pickering-stabilised by UiO-66 and magnetite nanoparticles as a template around which to deposit a hierarchically structured ZIF-8 shell. The resulting microcapsules are robust, highly microporous and readily attracted to a magnet, where the hydrogel core provides a facile means to encapsulate enzymes for recyclable size-selective biocatalysis.