An embodiment of the present disclosure provides an apparatus for immobilizing a microbial cell, the apparatus including: a mixing tank in which a cell-carrier-containing mixed solution is accommodated; a nozzle part through which the cell-carrier-containing mixed solution is injected from the mixing tank and is discharged to the outside; and a reaction tank in which a cell immobilized bead is formed by contact between the cell-carrier-containing mixed solution discharged from the nozzle part and an aqueous curing agent solution. In the apparatus for immobilizing a microbial cell according to the present disclosure, since the cell-carrier-containing mixed solution is injected through an air spraying nozzle, even when an immobilized carrier solution having a high viscosity is used, a microbial cell immobilized bead having a small size and having a spherical shape, or an almost spherical shape may be mass-produced.