With the tremendous growth of the halal industry, many non-dominant Muslim countries particularly Japan, have shown interest to tap into the halal market. To ensure the availability of halal products, therefore, it is crucial to have a comprehensive and well-managed halal supply chain. Integrating both “halal” (permissible) and “tayyib” (wholesome) throughout all the phases in the supply chain indicates that halal-certified companies need to comply with certain sustainability practices which are aligned with the halal certification systems. Nevertheless, there is always curiosity among the customers on the halal integrity across the supply chain and they will feel more confident if the products are halal certified. Apparently, halal certification bodies played a significant role to enhance the sustainable performance measures in the halal supply chain.  Currently, there are more than 30 halal certification bodies (HCBs) in Japan. Their backgrounds are diverse from Muslim local residents and community members in Japanese cities and individual Muslim academics specializing in agriculture and food systems, to Japanese businesspersons who are familiar with Islamic countries and religious organizations. Despite the vast opportunities, inevitably there are numerous challenges faced by the HCBs that may influence the sustainability of the halal supply chain in Japan. Hence, this motivates this paper to explore the management of the halal certification process and how it may affect halal supply chain sustainability. Based on the in-depth interviews with 5 established HCBs, this paper aims to explore the sustainable practices and the challenges in the halal supply chain that may contribute to the betterment of the halal industry in Japan.