The immunological and the anti-Leishmania amazonensis activity of babassu-loaded poly(lactic-co-glycolic acid) [PLGA] microparticles was evaluated. The anti-Leishmania activity was evaluated against promastigotes or amastigotes forms, in Balb/c macrophages. The size of the microparticles ranged from 3 to 6.4 μm, with a zeta potential of −25 mV and encapsulation efficiency of 48%. The anti-Leishmania activity of the PLGA microparticles loaded with the aqueous extract of babassu mesocarp (MMP) (IC50) was 10-fold higher than that free extract (Meso). MMP exhibited overall bioavailability and was very effective in eliminating intracellular parasites. MMP also reduced ex vivo parasite infectivity probably by the increased production of nitric oxide, hydrogen peroxide, and TNF-α indicating the activation of M1 macrophages. The overexpression of TNF-α did not impair cell viability, suggesting antiapoptotic effects of MMP. In conclusion, babassu-loaded microparticles could be useful for drug targeting in the treatment of leishmaniasis, due to the immunomodulatory effect on macrophage polarization and the increased efficacy as an anti-Leishmania product after the microencapsulation. These findings are of great relevance since the development of new drugs for the treatment of neglected diseases is desirable, mainly if we consider the high morbidity and mortality rates of leishmaniasis worldwide.