Polymeric beads have been used for protection and delivery of bioactive materials, such as drugs and cells, for different biomedical applications. Here, we present a generic two-phase system for the production of polymeric microbeads of gellan gum or alginate, based on a combination of in situ polymerization and phase separation. Polymer droplets, dispensed using a syringe pump, formed polymeric microbeads while passing through a hydrophobic phase. These were then crosslinked, and thus stabilized, in a hydrophilic phase as they crossed through the hydrophobic-hydrophilic interface. The system can be adapted to different applications by replacing the bioactive material and the hydrophobic and/or the hydrophilic phases. The size of the microbeads was dependent on the system parameters, such as needle size and solution flow rate. The size and morphology of the microbeads produced by the proposed system were uniform, when parameters were kept constant. This system was successfully used for generating polymeric microbeads with encapsulated fluorescent beads, cell suspensions and cell aggregates proving its ability for generating bioactive carriers that can potentially be used for drug delivery and cell therapy.