Expectations of exporting food and agricultural product to Malaysia have been substantially growing in Japan. Although Japan has two halal certification bodies recognized by Jabatan Kemajuan Islam Malaysia (JAKIM), it is unclear whether Malaysian consumers trust its certified processed foods. Thus, this study aims to clarify Malaysian consumers’ preference for Hokkaido ice cream by conducting a conjoint analysis. The results show no significant difference in the level of consumer trust in halal certifications, indicating a distribution based on both Malaysian and Japanese certification bodies. Therefore, it is possible that Malaysian consumers would accept Japanese products with a halal certification approved by JAKIM. In addition, the willingness to pay for Hokkaido ice cream reported a high satisfaction value. However, there is no significant effect on food functionality possibly because Malaysian consumers’ awareness of the health benefits remains low.