Precision fermentation, essential for manufacturing customized fermented foods, demands advanced technologies for precise control of fermentation microorganisms. Current methods fall short in regulating the type and number of microorganisms to desired levels. To address this limitation, we propose a novel approach using hydrogel-based polymer networks for microorganism control. Our method involves a hydrogel system with a biocompatible multilayer tough shell and a co-axial alginate and pectin-based inner core, effectively immobilizing yeast cells within the viscous core. This cell-containing polymeric hydrogel functions as a living material, forming a ‘cell factory’ where cells metabolize while being physically contained, preventing yeast leakage for more than 120 hours and providing an optimal environment for cell culture. This innovative biocontainment strategy allows metabolites to diffuse while spatially and temporally separating microorganisms, thus enabling precise fermentation control. Our study bridges material science and biology, offering a new microbial control model that could revolutionize biosensor development and biomanufacturing technologies.