We report on the synthesis of chitosan-alginate nanodisks (Cs-Al NDs) using a simple approach consisting of the ionotropic gelation method. Sodium tripolyphosphate (STPP) was used as crosslinking agent to promote the electrostatic interaction between amine groups the chitosan and hydroxyl and carboxyl groups of alginate. Scanning electron microscopy (SEM) images provided direct evidence of the morphology of the nanodisks where agglomeration was observed due to the electrostatic interaction between the functional groups. Furthermore, dynamic light scattering (DLS) showed that the hydrodynamic size of the Cs-Al NDs was 227 nm and 152 nm in pH 1.2 and pH 7.4, respectively, which is in agreement with the information observed in the SEM images. The chemical structure is presented mainly the amine and carboxyl groups due to the presence of chitosan and alginate in the nanodisks, respectively, which allow the electrostatic interaction through N-H linkages. According to the X-ray diffraction, we found that the Cs-Al NDs exhibited the typical structure of chitosan and alginate, which lead the formation of polyelectrolyte complexes. We also evaluated the encapsulation of amoxicillin in the nanodisk, obtaining a loading efficiency of 74.98%, as well as a maximum in vitro release amount of 63.2 and 52.3% at pH 1.2 and 7.4, respectively. Finally, the cytotoxicity effect of the Cs-Al nanodisks was performed in human prostatic epithelial PWR-1E and Caucasian prostate adenocarcinoma PC-3 cell lines, in which the cell viability was above 80% indicating low inhibition and determining the Cs-Al NDs as a promising technology for controlled delivery systems.