Nanoengineered poly(methacrylic acid) hydrogel capsules (PMA HCs) are promising candidate carriers for biomedical applications, especially in the areas of drug delivery, encapsulated catalysis, and cell mimicry. The assembly, stability, and degradation Of these carriers, as well as their use for the encapsulation of therapeutics, have received considerable attention. However, tailoring the permeability properties of PMA HCs to various types of cargo remains largely unexplored. Herein, we investigate fundamental parameters that govern the structural integrity and the capability of PM A HCs to encapsulate macromolecular cargo. The thiol content of the constituent polymers and the number of deposited polymer layers are shown to be key factors in controlling cargo retention within the PMA HCs. We further introduce a new strategy to achieve disulfide cross-linking for PMA HCs via a thiol disulfide exchange in order to obtain capsules with superior cargo retention characteristics. Finally, we provide evidence for the semipermeable nature of PMA HCs based on the charge of the solutes and demonstrate that rational design of these systems can yield capsules with specific cargo retention properties. This work contributes toward the development of multilayered polymer capsules and PMA HCs and associated applications in biomedicine.