A next-generation cure for type 1 diabetes relies on immunoprotection of insulin-producing cells, which can be achieved by their encapsulation in microspheres made of non-covalently crosslinked hydrogels. Treatment success is directly related to the microsphere structure that is characterized by the localization of the polymers constituting the hydrogel material. However, due to the lack of a suitable analytical method, it is presently unknown how the microsphere structure changes in vivo, which complicates evaluation of different encapsulation approaches. Here, confocal Raman microscopy (CRM) imaging was tailored to serve as a powerful new tool for tracking structural changes in two major encapsulation designs, alginate-based microbeads and multi-component microcapsules. CRM analyses before implantation and after explantation from a mouse model revealed complete loss of the original heterogeneous structure in the alginate microbeads, making the intentionally high initial heterogeneity a questionable design choice. On the other hand, the structural heterogeneity was conserved in the microcapsules, which indicates that this design will better retain its immunoprotective properties in vivo. In another application, CRM was used for quantitative mapping of the alginate concentration throughout the microbead volume. Such data provide invaluable information about the microenvironment cells would encounter upon their encapsulation in alginate microbeads.