To find out natural antimicrobial agents as alternative in therapeutics and to preserve food, the methanol extract of Solanum palinacanthum aerial parts was submitted to purification steps guided by antibacterial and antifungal assays. As a consequence, the flavonoid rutin and 3,5-dicaffeoylquinic acid were isolated by column chromatography and high performance liquid chromatography, and identified by mass and nuclear magnetic resonance spectrometry. Minimal inhibitory concentrations (MIC) of the quinic acid derivative against Aeromonas hydrophila, Bacillus subtilis, Staphylococcus aureus and the fungus Aspergillus ochraceus were 250, 1000, 1000 and > 568 microg/mL, respectively. Against the same microorganisms, MIC for rutin were 1000, > 1000, > 1000 and 35 microg/mL, respectively. Rutin was very promising for A. ochraceus control, since its MIC against such fungus was close to the one observed for benzalkonium chloride, which is used as a fungicide in Brazil.