This study demonstrates the successful manufacture and functional characterization of alginate hydrogels containing a variety of encapsulates within polyelectrolyte multilayer-coated micropores. These microporous alginate (MPA) hydrogels are prepared via one-step internal ionotropic gelation of the alginate using polyelectrolyte multilayer-coated CaCO3 microspheres along with the weak acid glucono-δ-lactone. Here, successful encapsulation of a model macromolecule and fluorescent nanoparticles within microcapsules—distributed throughout the larger alginate hydrogel—is confirmed with confocal microscopy, while the porous morphology of the MPA hydrogels is examined with scanning electron microscopy. Hydrogels constructed with uncoated CaCO3 microspheres release their contents into the surrounding environment, while those constructed with polyelectrolyte multilayer-coated CaCO3 microspheres retain the materials within the pores. MPA hydrogels containing the model enzyme glucose oxidase retained activity and are capable of reacting with small molecules from the external environment. The ability to encapsulate an assortment of functional materials within a moldable, biocompatible alginate matrix gives this approach great flexibility and potential in a wide variety of biomedical applications.