Astaxanthin Z-isomers potentially have greater bioavailability and biological activity than (all-E)-astaxanthin. However, the stability of the Z-isomers is lower than the all-E-isomer, which is a serious problem affecting its practical use. In this study, we investigated the impacts of different suspension media (oils and fats) and additives on astaxanthin isomer stability and identified suitable ones for astaxanthin stabilization. The evaluations showed that several vegetable oils and antioxidants significantly improved astaxanthin isomer stability, e.g., when soybean and sunflower oils were used as the suspension medium, astaxanthin isomers were hardly degraded; however the total Z-isomer ratio decreased from ~80% to ~50% during 6-week storage at 30 °C. Moreover, it was revealed that (9Z)-astaxanthin showed higher stability than the 13Z- and 15Z-isomers. Hence, to maintain astaxanthin concentration and the Z-isomer ratio over long periods, it is important to use suitable suspension mediums and antioxidants, and select a Z-isomerization method that increases (9Z)-astaxanthin ratio.