Encapsulation of proteins in polymeric matrices can offer protection from enzymatic degradation upon oral administration, and thus protein bioavailability can be improved. Interpolyelectrolyte complexation is used to modify the performance of the polymers in terms of solubility, permeability and swelling. In this study, bovine serum albumin (BSA), as a model protein, was loaded into microparticles of carrageenan-Eudragit E interpolyelectrolyte complex and chitosan-laurate a hydrophobic salt of chitosan. The microparticles were characterized for drug encapsulation efficiency and particle size. The drug release from the microparticles was studied in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF). Digestibility of the protein as solution and as dispersion of the protein loaded microparticles was examined using a newly developed method that can separate the digestion products from the intact protein. The microparticles were shown to have acceptable particle size and satisfactory drug loading efficiency. The protein release from EE-CG microparticles was slower than that from chitosan-laurate and was characterized by being biphasic with burst release followed by slow BSA release. In comparison to BSA as aqueous solution, the encapsulated protein in the EE-CG microparticles showed a slower rate of enzymatic degradation by pepsin and pancreatin. However, an enhancement of BSA digestion occurred when it was loaded in chitosan-laurate microparticles, which was explained in terms of enzyme immobilization onto the microparticle matrix.