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Sea buckthorn (<i>Hippophae rhamnoides</i> L.) represents a valuable source of biologically active compounds such as carotenoids and polyphenols. High amounts of these substances are found in its fruits, bark, and leaves. However, their bioavailability is limited and must be increased in order to benefit from the properties they exert. Therefore, the purpose of this study was to increase the stability and bioavailability of sea buckthorn fruit’s bioactives. The sea buckthorn’s bioactive compounds were extracted with a solvent combination between glacial acetic acid, acetone, and water on one side and water only on the other side. Afterward, the phytochemicals from the extracts were encapsulated using the coacervation technique, followed by freeze-drying in order to obtain stable powders. The powders were characterized in terms of antioxidant activity, total carotenoids, β-carotene, lycopene, total polyphenol, and total flavonoid content, color, structure, and morphology. The phytochemical stability of the powders and their antioxidant activity was assessed during 270 days of storage at 4 °C. Moreover, the bioavailability of phytochemicals was measured during in vitro simulated digestibility. Our findings provide insights to promote carotenoids and polyphenols from sea buckthorn as bioactive ingredients with multiple purposes.