C-phycocyanin (CPC) is an antioxidant protein that, when purified, is photosensitive and can be affected by environmental and gastrointestinal conditions. This can impact its biological activity, requiring an increase in the effective amount to achieve a therapeutic effect. Therefore, the aim of this study was to develop a microencapsulate of a complex matrix, as a strategy to protect and establish a matrix for the controlled release of CPC based on polysaccharides such as agavins (AGV) using ionic gelation. Four matrices were formulated: M1 (alginate: ALG), M2 (ALG and AGV), M3 (ALG, AGV, and κ-carrageenan: CGN), and M4 (ALG, AGV, CGN, and carboxymethylcellulose: CMC) with increasing concentrations of CPC. The retention and diffusion capacities of C-phycocyanin provided by each matrix were evaluated, as well as their stability under simulated gastrointestinal conditions. The results showed that the encapsulation efficiency of the matrix-type encapsulates with complex composites increased as more components were added to the mixtures. CMC increased the retention due to the hydrophobicity that it provides by being in the polysaccharide matrix; CGN enabled the controlled diffusive release; and AGV provided protection of the CPC beads under simulated gastrointestinal conditions. Therefore, matrix M4 exhibited an encapsulation efficiency for CPC of 98% and a bioaccessibility of 10.65 ± 0.65% after the passage of encapsulates through in vitro digestion.