Carotenoid Z-isomers exhibit higher bioavailability and potentially beneficial biological activities than their all-Eisomers, which predominate in nature. However, they are chemically unstable and poorly soluble in water, which hinder the practical use of Z-isomer-enriched carotenoid materials. Encapsulating carotenoid Z-isomers in water-soluble carriers can overcome these problems. Here, we successfully prepared Zisomer-enriched carotenoids (lycopene, β-carotene, and astaxanthin)/poly(vinylpyrrolidone) (PVP, a water-soluble polymer) inclusion complexes using a continuous-flow system which is constituted of a heated flow reactor and a spray dryer. Processing in the flow reactor at 200 °C for 15 s prior to spray drying improved the total Z-isomer ratio of the encapsulated carotenoids (>55%) and encapsulation efficiency of carotenoids in PVP. Furthermore, storage tests of the resulting complexes demonstrated that formulating (Z)-carotenoids with PVP stabilized their Z-structures. The results of this study contribute to the realization of industrial applications of Z-isomer-enriched carotenoids with great utility and health benefits.