The bioactivity of carotenoids and tocols is limited by their instability, hydrophobicity, and low bioavailability. Hence, the study aimed to design microspheres from sea buckthorn juice by ionotropic gelation to increase stability, ensure high content of carotenes, xanthophylls, tocopherols and tocotrienols and their antidiabetic activity. The effects of biopolymers, cross-linking and storage on the carotenoid and tocol profile of microspheres (identified and quantified by LC-PDA-QTOF-ESI-MS and UPLC-FL methods) and their in vitroα-amylase and α-glucosidase inhibitory activity were investigated. Microspheres containing sodium alginate/κ-carrageenan (4:1) had significantly high content of carotenoids and tocols, and antihyperglycemic activity (p < 0.05). The two-step cross-linking (1-calcium chloride, 2-chitosan) provided a 17% higher carotenoid content. Cross-linking with CaCl2 promoted high content of tocopherols but stability protection was provided by sodium alginate and CaCl2/chitosan (9:1) cross-linking (1.7-fold decrease in instability). The encapsulation using newly designed combinations of biopolymers and cross-linking could be an effective strategy to increase the stability and bioactivities of microspheres as nutraceuticals and smart food.