Having previously highlighted the gelation of pectin with chlorhexidine (CX), pectinate microparticles were prepared here by vibrational prilling using CX, not only as an active ingredient encapsulated but also as a cross-linking agent. CX amount required for pectin gelation was smaller than usual dications (Ca2+, Zn2+) used as cross-linking agent for pectin ionotropic gelation: CX seemed to bind more easily to pectin chains that could be explained by its large molecular size. Three batches of CX microparticles with different mean size were prepared. Whatever the droplet mean diameter, similar particle characteristics in terms of encapsulation efficiency, CX encapsulation yield and drug release were observed. The encapsulation efficiency was about 5.5%, the CX encapsulation yield was approximately 44% and the maximal amount of CX released after 6 h was about 7%. Finally, zinc diacetate was added to the formulation as a competitive pectin cross-linking agent in order to limit CX binding to pectin and to improve CX release. The influence of CX and Zn2+ concentrations on the particles properties was studied by the means of a Doehlert design. Results showed the interest of such a mixture since the competition between both cations led to more or less structured and large microparticles, some of them having promoted the quantity of CX released.