Currently, in developing countries, parasitic and bacterial diseases as amebiasis, giardiasis, trichonomiasis, leishmaniasis, trypanosomiasis, tuberculosis, and nocardiasis are a public health problem. The pharmacological treatment for these diseases is not completely effective and causes several side effects in patients. Therefore, the searchfor new compounds with biological activity is very important to develop new drugs safely and more efficiently. In this study, different organic extracts obtained from thirty-seven species of the Salvadoran flora were evaluated in several in vitromodels to determine their potential activity against five protozoa (Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, Leishmania mexicana, and Trypanosoma cruzi) and three bacteria (Acinetobacter baumanni, Mycobacterium tuberculosis, and Nocardia brasiliensis). The results showed the activity of eight extracts with IC50values of less than 100 μg/mL against L. mexicanaand five extracts with MICs values less than <50 μg/mL against M. tuberculosis. Besides, seven plant species showed MICs ≤3.125 μg/mL against N. brasiliensis. Additionally, secondary metabolites (flavonoids and monoterpene oxygenate) previously reported as active were fingerprint by UPLC-MS to establish a potential correlation with the biological activity showed.