The present work aims to encapsulate goby fish protein hydrolysate (GPH), endowed with antioxidant activity, through ionic gelation process using blue crab chitosan (CH) and tripolyphosphate anions and to evaluate the structural, thermal and antioxidant properties of the elaborated microparticles (MPs). The GPH-loaded MPs present spherical shape as seen by scanning electron microscopy (SEM) images and positive zeta potential. The increase of loaded GPH concentration led to the increase of encapsulation efficiency (EE) and to the reduction of the particle size. In fact, MPs, loaded with 2 and 5 mg/ml GPH, had EE values of 44 and 58% and mean particles size of 4.81 and 3.78 μm, respectively. Furthermore, thermogravimetric analysis (TGA) profiles revealed the enhanced thermal stability of encapsulated biopeptides compared to the free ones. Release kinetic data showed a Fickian diffusion behavior which follows swelling and a diffusion-controlled mechanism for peptides liberation. Finally, as opposed to unloaded MPs, an improvement of the antioxidant activity of the loaded MPs with biopeptides was observed.