Research on microalgae-nitrifying bacteria has increased due to their ability to remove nitrogen without expensive mechanical aeration. However, due to photosensitivity of nitrifying bacteria, their outdoor application in certain environments can lead to poor treatment performance or process breakdown. Hence, we developed a light-shielding hydrogel encapsulating nitrifying bacteria to form a light-tolerant microalgae-nitrifying bacterial consortium. The established light-tolerant microalgae-nitrifying bacteria consortium can successfully remove ammonia even under bright light conditions. Batch experiments were conducted using light-tolerant microalgae-nitrifying bacteria consortia under 500 µmol photons m−2 s−1 to evaluate the effects of biomass ratios on the microalgal growth and ammonia removal. The maximum specific growth rate of microalgae, i.e. 1.3 d−1 was obtained for a biomass ratio (microalgae: nitrifying bacteria) of 1:9. Multiple regression analysis also revealed that the abundance of nitrifying bacteria was associated with a higher ammonia removal efficiency than microalgae. These findings can be used to design an effective treatment process for removing high concentrations of ammonia by microalgae-nitrifying bacteria consortia exposed to intense light.