Chitosan-alginate microparticles loaded with hydrophobic mangostins present in the mangosteen rind extract have been formulated and optimized for colon-targeted bioactive drug delivery systems. The chitosan–mangostin microparticles were prepared using the ionotropic gelation method with sodium tripolyphosphate as the cross-linking agent of chitosan. The chitosan–mangostin microparticles were then encapsulated in alginate with calcium chloride as the linking agent. The mangostin release profile was optimized using the Box–Behnken design for response surface methodology with three independent variables: (A) chitosan–mangostin microparticle size, (B) alginate:chitosan mass ratio, and (C) concentration of calcium chloride. The following representative equation was obtained: percent cumulative release of mangostins (10 h) = 59.51 − 5.16A + 20.00B − 1.27C − 1.70AB − 5.43AC − 5.04BC + 0.0579A2 + 10.25B2 + 1.10C2. Cumulative release of 97% was obtained under the following optimum condition for microparticle preparation: chitosan–mangosteen particle size < 100 µm, alginate:chitosan mass ratio of 0.5, and calcium chloride concentration of 4% w/v. The alginate to chitosan mass ratio is the statistically significant variable in the optimization of sequential release profile of mangostins in simulated gastrointestinal fluids. Furthermore, a sufficient amount of alginate is necessary to modify the chitosan microparticles and to achieve a complete release of mangostins. The results of this work indicate that the complete release of mangostins to the colon area can be achieved using the chitosan–alginate microparticles as the bioactive delivery system.