More recently, single-cell encapsulation emerged as a promising field in biomedicine due to its potential applications, in cell analysis and therapy. Traditional techniques involve embedding cells in crosslinked polymers to create continuous microgels, suitable mainly for adherent cells, or encapsulating them in droplets for only short-term analysis, due to their instability. In this study, we developed a method for encapsulating single cells in liquid-core microcapsules to address these limitations. The liquid encapsulation system is generated in an all aqueous environment through polymeric electrostatic interactions. Additionally, we design an innovative and low cost sorting system utilizing magnetic nanoparticles (MNPs) to efficiently select single-cell encapsulated units for further analysis and applications. This system is tested with both suspension and adherent cell types, demonstrating cytocompatibility and no abnormal effects on cell behavior. The MNP-based sorting achieved nearly 80% purity of the single-cell population. Overall, this technology provides a highly efficient method for single-cell applications, such as cell screening, by enabling precise short to medium-term analysis, real time monitoring, and high resolution imaging of cellular behavior. Furthermore, the semipermeable membrane unlocks new potential for advancing cell therapy by offering protection for encapsulated cells while ensuring the efficient diffusion of therapeutic factors, paving the way for innovative therapeutic strategies.