A core-shell structured poly(vinyl alcohol)/sodium alginate gel bead was fabricated and the thickness of the outer layer was controlled. Immobilized ammonia-oxidizing bacteria (AOB) and ANAMMOX bacteria in outer and inner parts of the beads, respectively, cooperate to perform single-stage autotrophic nitrogen removal (SANR). As a critical designing factor, oxygen penetration depth according to the oxygen concentration in bulk phase and nitrifying biomass concentration in the outer layer were examined to protect strictly anaerobic ANAMMOX bacteria from oxygen inhibition. Oxygen penetrated up to a depth of 2350 ± 360 μm with the lowest nitrifying biomass of 703 mg-VSS/L at a dissolved oxygen concentration of 8 mg/L. However, a thick shell layer of more than 3 mm effectively protected the ANAMMOX bacteria from oxygen inhibition. The applicability of the core-shell structured gel bead for single-stage autotrophic nitrogen removal was validated in batch and continuous modes. A continuous bioreactor with a synthetic ammonia wastewater showed a maximum nitrogen removal efficiency of 80.4 ± 1.20% with a total nitrogen loading rate of 590 ± 12.1 g-N/m³-d. Findings of this study suggest that start-up strategy of SANR using the core-shell structured gel bead can minimize the adaptation period without scarifying the ANAMMOX activity.