Due to the resistance to drugs, studies involving the combination and controlled release of different agents are gradually increasing. In this study, two different active ingredients, known to have antibacterial and antiparasitic activities, were encapsulated into single polymeric nanoparticles. After co-encapsulation their antibacterial and antileishmanial activity was enhanced approximately 5 and 250 times, respectively. Antibacterial and antileishmanial activities of caffeic acid phenethyl ester and juglone loaded, multifunctional nanoformulations (CJ4-CJ6-CJ8) were also evaluated for the first time in the literature comparatively with their combined free formulations. The antibacterial activity of the multifunctional nanoformulation (CJ8) were found to have a much higher activity (MIC values 6.25 and 12.5 mu gml(-1) for S. aureus and E. coli, respectively) than all other formulations. Similar efficacy for CJ8 was obtained in the antiparasitic study against the Leishmania promastigotes and the IC50 was reduced to 0.1263 mu gml(-1). The high activity of multifunctional nanoparticles is not only due to the synergistic effect of the active molecules but also by the encapsulation into polymeric nanoparticles. Therefore, it has been shown in the literature for the first time that the biological activity of molecules whose activity is increased by the synergistic effect can be improved with nanosystems.