A series of isoxazole and triazole derivatives, with interesting bioactive scaffolds, were examined for their in vitro antibacterial, antifungal, and antiprotozoal activities. These compounds exhibited antitrypanosomal activity comparable to difluoromethylornithine (DMFO), a drug used in the treatment of human African trypanosomiasis. Isoxazole analogues 1, 3 and 4, and triazole derivatives 16, 17, 28, 37, 40 and 42 showed the highest antitrypanosomal activity with IC50 values of 17.89, 1.82, 10.38, 10.26, 11.77, 9.29, 3.93, 2.11, and 0.93 μM, respectively. Compounds 40 and 42 showed the most potent activity against Leishmania donovani amastigotes with IC50 values of 18.28 and 10.54 μM, respectively. Compound 42 showed the most potent activity against Leishmania donovani macrophage internalized amastigotes with an IC50 value of 8.32 μM. Conjugate triazoles 40–43 displayed potential antimalarial activity against chloroquine-resistant W2 and chloroquine sensitive D6 Plasmodium falciparum strains (IC50 value range from 0.58 to 8.36 μM). Compound 37 showed antibacterial activity against Staphylococcus aureus, MRSA and Mycobacterium intracellulare with IC50 values of 15.53, 14.22 and 47.45 μM, respectively. None of the compounds exhibited antifungal activity.