The effect of ultrasonic treatments of different intensity and duration on the integrity and permeability of polyelectrolyte capsules was investigated both in poly(allylamine)/poly(styrene sulfonate) and Fe3O4/poly(allylamine)/poly(styrene sulfonate) polyelectrolyte capsules. Ultrasonic treatment of polyelectrolyte capsules induces the destruction of the polyelectrolyte shell and the release of the encapsulated material even at short (5 s) sonification times. The presence of magnetite nanoparticles significantly improves the efficiency of the ultrasonically stimulated release of the encapsulated compounds and enables magnetically controlled delivery to the desired site before ultrasonic treatment. Release of the encapsulated compound induced at ultrasonic power comparable to those of ultrasonic generators applied in medicine, demonstrating practical application of the ultrasonically triggered capsule opening in medicine.