Enzyme-catalyzed degradation of CaCO₃-templated capsules is presented. We investigate a) biodegradable, b) mixed biodegradable/synthetic, and c) multicompartment polyelectrolyte multilayer capsules with different numbers of polymer layers. Using confocal laser scanning microscopy we observed the kinetics of the non-specific protease Pronase-induced degradation of capsules is slowed down on the order of hours by either increasing the number of layers in the wall of biodegradable capsules, or by inserting synthetic polyelectrolyte multilayers into the shell comprised of biodegradable polymers. The degradation rate increases with the concentration of Pronase. Controlled detachment of subcompartments of multicompartment capsules, with potential for intracellular delivery or in-vivo applications, is also shown.