Interparticle agglomeration is challenging for developing amorphous β-carotene highly loaded microcapsules. Herein, they were innovatively fabricated by a combination of wet-milling and spray drying. The impact of complexed wall materials on inhibition of interparticle agglomeration, recrystallisation behavior, redispersibility and bioaccessibility of β-carotene was surveyed. The optimal β-carotene microcapsules presented a fine particle size when rehydrated (350.1 nm) with a high encapsulation efficiency and loading capacity (98.52% and 13.93%, respectively). Both interparticle agglomeration during spray drying and recrystallisation during storage of amorphous β-carotene were well hindered because of the complexation between wall materials. The mean diameter of microcapsules was also decreased from 12.0 to 7.3 μm when the compactness of wall materials was enhanced, and the wrinkles located at the external surface of microcapsules promoted water permeation upon reconstitution. Furthermore, the release profile and bioaccessibility of β-carotene in microcapsules were greatly enhanced owing to the preferable micellization process and solubilization capacity of amorphous β-carotene.