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Abstract Black soybean peels (BSPs) are rich in anthocyanins (ANCs), a naturally active substance added to manufactured foods. However, the instability of the ANC structure limits its application in the food industry. In the present study, an efficient and simple microencapsulation method to improve the stability of ANC was successfully established. BSP ANCs were encapsulated in a microencapsulated complex with fructo‐oligosaccharide (FOS) and whey protein (WP) associated with a high encapsulation rate (65.41%) and drug‐loading capacity (6.13%). The particle size and polydispersity index of anthocyanin‐loaded microencapsulation (ALM) were 4.648 ± 0.350 µm and 0.405 ± 0.107, respectively. The ANC stability test showed that ALM performed enhanced thermostability, pH stability, storage stability, and light stability. Meanwhile, in vitro release experiments indicated that ALM dramatically delayed the contact time of ANC with the environment and reduced the degradation. Moreover, animal experiments demonstrated that ALM better improved blood glucose homeostasis and lipid homeostasis in high‐fat‐ and high‐fructose‐treated mice and reduced liver lipid accumulation and damage. Additionally, the better in vivo bioactivity could be attributed to the extended bioavailability that was proved by a pharmacokinetics test. These results suggested that the microencapsulation employed WP‐FOS complexes as the wall materials are of great potential to improve the stability and health‐promoting properties of ANC, providing a promising solution as dietary supplementation.