Carotenoids are naturally occurring pigments whose presence in the diet is beneficial to human health. Moreover, they have a wide range of applications in the food, cosmetic, and animal feed industries. As carotenoids contain multiple conjugated double bonds in the molecule, a large number of geometric (E/Z, trans/cis) isomers are theoretically possible. In general, (all-E)-carotenoids are the most predominant geometric isomer in nature, and they have high crystallinity and low solubility in various mediums, resulting in their low processing efficiency and bioavailability. Technological developments for improving the processing efficiency and bioavailability of carotenoids utilizing the Z-isomerization have recently been gaining traction. Namely, Z-isomerization of carotenoids induces a significant change in their physicochemical properties (e.g., solubility and crystallinity), leading to improved processing efficiency and bioavailability as well as several biological activities. For the practical use of isomerization technology for carotenoids, the development of efficient isomerization methods and an acute understanding of the changes in biological activity are required. This review highlights the recent advancements in various conventional and unconventional methods for carotenoid isomerization, such as thermal treatment, light irradiation, microwave irradiation, and catalytic treatment, as well as environment-friendly isomerization methods. Current progress in the improvement of processing efficiency and biological activity utilizing isomerization technology and an application development of carotenoid Z-isomers for the feed industry are also described. In addition, future research challenges in the context of carotenoid isomerization have been elaborated upon.