Polymer microcarriers are being extensively explored as cell delivery vehicles in cell-based therapies and hybrid tissue and organ engineering. Spherical microcarriers are of particular interest due to easy fabrication and injectability. They include microbeads, composed of a porous matrix, and microcapsules, where matrix core is additionally covered with a semipermeable membrane. Microcarriers provide cell containment at implantation site and protect the cells from host immunoresponse, degradation and shear stress. Immobilized cells may be genetically altered to release a specific therapeutic product directly at the target site, eliminating side effects of systemic therapies. Cell microcarriers need to fulfil a number of extremely high standards regarding their biocompatibility, cytocompatibility, immunoisolating capacity, transport, mechanical and chemical properties. To obtain cell microcarriers of specified parameters, a wide variety of polymers, both natural and synthetic, and immobilization methods can be applied. Yet so far, only a few approaches based on cell-laden microcarriers have reached clinical trials. The main issue that still impedes progress of these systems towards clinical application is limited cell survival in vivo. Herein, we review polymer biomaterials and methods used for fabrication of cell microcarriers for in vivo biomedical applications. We describe their key limitations and modifications aiming at improvement of microcarrier in vivo performance. We also present the main applications of polymer cell microcarriers in regenerative medicine, pancreatic islet and hepatocyte transplantation and in the treatment of cancer. Lastly, we outline the main challenges in cell microimmobilization for biomedical purposes, the strategies to overcome these issues and potential future improvements in this area.