The effect of postmodification of polyelectrolyte multilayer microcapsules by exposure to organic solvent/water mixtures on their permeability, morphology, and mechanical properties is investigated. We study microcapsules with ultrathin shells composed of alternating polystyrene sulfonate and polyallylamine hydrochloride. Ethanol and acetone are used as organic solvents. In pure water, the high-molecular-weight dextran cannot diffuse through the shells of microcapsules. However, the addition of even a small amount of ethanol or acetone allows its fast encapsulation. We demonstrate that a mechanism of encapsulation in ethanol and acetone solutions is fundamentally different. In case of ethanol/water mixtures, the reason for encapsulation is the contraction of coils of the encapsulated polymer. No changes in the shell morphology, its nanopore structure, or mechanical properties as compared with those in pure water were detected. In contrast, in the case of acetone/water mixtures, the encapsulation reflects the true permeability changes of the shells caused by a formation of large nanopores, This is accompanied by a significant softening of the capsules. Our results suggest that electrostatic screening caused by addition of organic solvent does not play any significant role in the control of permeability and mechanical properties of polyelectrolyte multilayer microcapsules.