Xylella fastidiosa is a plant-pathogenic bacterium that lives inside host xylem vessels, where it forms biofilm which is believed to be responsible for disrupting the passage of water and nutrients. Pectobacterium carotovorum is a Gram-negative plant-specific bacterium that causes not only soft rot in various plant hosts, but also blackleg in potato by plant cell wall degradation. Chagas disease, which is caused by Trypanosoma cruzi, has been commonly treated with nifurtimox and benzonidazole, two drugs that cause several side effects. As a result, the use of natural products for treating bacterial and neglected diseases has increased in recent years and plants have become a promising alternative to developing new medicines. Therefore, this study aimed to determine, for the first time, the chemical composition of essential oil from Psidium guajava flowers (PG-EO) and to evaluate its in vitro anti-Xylella fastidiosa, anti-Pectobacterium carotovorum, anti-Trypanosoma cruzi and cytotoxic activities. PG-EO was obtained by hydrodistillation in a Clevenger apparatus while its chemical composition was determined by gas chromatography-flame ionization detection (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Major compounds identified in PG-EO were α-cadinol (37.8%), β-caryophyllene (12.2%), nerolidol (9.1%), α-selinene (8.8%), β-selinene (7.4%) and caryophyllene oxide (7.2%). Results showed that the PG-EO had strong trypanocidal activity against the trypomastigote forms of Trypanosoma cruzi (IC50 = 14.6 μg/mL), promising antibacterial activity against X. fastidiosa (MIC = 12.5 μg/mL) and P. carotovorum (MIC = 62.5 μg/mL), and moderate cytotoxicity against LLCMK2 adherent epithelial cells in the concentration range (CC50 = 250.5 μg/mL). In short, the PG-EO can be considered a new source of bioactive compounds for the development of pesticides and trypanocide drugs.