Resistance of microorganisms to commercial drugs is increasing worldwide, and therefore the search for new antimicrobial agents is a key issue. The aim of this study was to identify the potential of plant extracts from Ruta graveolens and Annona muricata as candidates for the development of new antimicrobials. Plant extracts were obtained by the Soxhlet method and their biological evaluation was carried out by the agar diffusion method, with 4 doses assayed (6.25, 25, 50 and 100 mg/mL) and 4 replicates per dose. Eight bacterial strains from American Type Culture Collection (ATCC) were tested: Escherichia coli O157 (ATCC 43894), Streptoccocus agalactiae (ATCC 13813), Salmonella enteritidis (ATCC BBA664), Enterobacter aerogenes (ATCC 13048), Staphylococcus aureus (ATTC 13565), Klebsiella pneumoniae (ATCC 4352), Proteus mirabilis (ATCC 14153) and Proteus vulgaris (ATCC 9484). Extracts from both plants showed antibacterial activity against all bacteria tested, with the exception of A. muricata extract against S. enteritidis. Minimum inhibitory concentration for both extracts was 6.25 mg/mL for E. aerogenes, S. agalactiae, S. aureus, and K. pneumoniae, 25 mg/mL for E. coli, P. mirabilis, and P. vulgaris, and 50 mg/mL of R. graveolens for Salmonella enteritidis. There were no differences between extracts in their antibacterial activity against P. vulgaris (P = 0.91) and K. pneumoniae (P = 0.37), but R. graveolens extract showed greater (P < 0.001) antibacterial activity against E. coli and S. agalactiae than A. muricata extract, and a trend was also observed for E. aerogenes (P = 0.064). In contrast, A. muricata extract tended to have greater (P = 0.094) antibacterial activity against P. mirabilis compared with R. graveolens extract. The results suggest that these extracts have active ingredients that could help to develop new antimicrobial products for the improvement of animal production and health.