The ability of chitosan and its derivatives to bind cations is well known. Chitosan and thiolated chitosan were recently associated with poly(isobutyl cyanoacrylate) (PIBCA) nanoparticles leading to very promising results in terms of bioadhesion and permeation enhancement properties. Taking into account the influence that cations concentration have in the maintenance of both the permeation and the enzymatic barrier of the oral route, the possible cation binding capacity of these colloidal systems might be interesting in the use of these nanocarriers for the oral administration of pharmacologically active peptides. The aim of the present work was to in vitro evaluate the capacity of these colloidal systems to bind calcium, a model cation of physiological interest in the intestinal tract. The presence of chitosan on the nanoparticle surface importantly increased the calcium binding ability, in comparison to non-coated PIBCA nanoparticles. In addition, its presentation in the gel layer surrounding the nanoparticles, also beneficiated its binding capacity, obtaining 2–3 folds higher values when the polymer coated the nanoparticles than when it was in solution. The cross-linked structure observed for thiolated chitosan, due to the formation of inter- and intra-chain disulphide bonds, diminished the accessibility of cation to active sites of the polymer, decreasing the binding capacity of the calcium ion. However, when the amount of free thiol groups on the nanoparticle surface was high enough, the binding behaviour observed was higher than for nanoparticles elaborated with non-modified polymer.