Bipolar membrane electrodialysis (BMED) has emerged as an efficient and promising technology for the removal and recovery of ammonia nitrogen. Despite its potential, the optimization of BMED systems for enhanced performance and energy efficiency remains a critical challenge, particularly in the context of varying ion exchange membrane (IEM) thicknesses. Membranes with a thickness of < 80 µm have low resistance and are mainly used for processes requiring low energy consumption. Membranes with a thickness of 80–250 µm have moderate resistance and high ion selectivity and are widely used for electrodialysis applications. Membranes with a thickness of > 250 µm have higher ion selectivity than commercial membranes with a thickness of 80–250 µm and are suitable for processes that demand high purity. This study investigates the effect of IEM thickness ranging from 16–400 µm on BMED performance for ammonia nitrogen removal and recovery, and energy consumption. The BMED configuration comprising five cell triplets consisting of a cation exchange membrane, bipolar membrane, and anion exchange membrane was employed. The thickness of IEMs was divided into three categories: 16–17 µm (PCEM/ PAEM), 100–150 µm (CD100/AD100, InnoSep-C/InnoSep-A), and 380–400 µm (MC-3470/MA-3475). In membranes with a thickness of 100–150 µm, the ammonia nitrogen removal was exceptionally high at 99.2 %, with a recovery of 98.7 % (CD100/AD100: 100 µm) at a current density of 80 mA/cm2, and the system exhibited low specific energy consumption (SEC) of 8.87 kWh/kg-N (InnoSep-C/InnoSep-A: 150 µm) at a current density of 20 mA/cm2. However, when using the thinnest IEMs (PCEM: 16 µm, PAEM: 17 µm), an increase in total ammonia nitrogen loss (10.21–22.01 %) led to a reduction in ammonia nitrogen recovery. Conversely, when using the thickest IEMs (MC-3470: 380 µm, MA-3475: 400 µm), the SEC was extremely high (30.98–126.67 kWh/kg-N), making them unsuitable for the BMED process for ammonia nitrogen removal and recovery. Based on these experimental results, it is suggested to use an optimal thickness of IEM within the range of 80–250 µm in the BMED systems to achieve a balanced performance, maximizing ammonia nitrogen removal and recovery while minimizing the SEC. Consequently, the present study provides a comprehensive understanding of the effects of the IEM thicknesses on the BMED systems and could offer a practical perspective for optimizing the BMED stack with respect to improving the removal and recovery rate of ammonia nitrogen and reducing the energy consumption.