Mulberry is a rich source of anthocyanins (ACNs) known to possess biological activities. However, these ACNs are unstable in high pH, heat, and aqueous environments with a low bioavailability. In this study, a colloidal dispersion was prepared by hot melt extrusion with proper excipients. In this process, a hydrophilic polymer matrix was used to confirm the stability of the compound in high pH, high temperature, and aqueous media. It was confirmed that the particle size and the polydispersity index value were reduced, thereby improving the solubility. In vitro release studies revealed that the extrudate had a sustained release compared to a non-extruded product. As a result of measuring changes of intestinal microorganisms (Lacticaseibacillus rhamnosus, Pediococcus pentosaceus, Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus), contents of probiotics were found to be increased whereas contents of pathogenic microorganisms were decreased. Thus, hot-melt extrusion could enhance the stability of ACN with prolonged release. The processed formulation exhibited probiotic properties and antimicrobial activities against pathogenic intestinal microflora.