Plants are prone to be attacked by various pathogenic microorganisms, leading to significant crop yield losses. Pesticides are used to control agricultural pathogens; however, frequently, they are toxic synthetic products. This work evaluated the antibacterial and antifungal activity of Pernettya prostrata, and Rubus roseus plant extracts against three phytopathogens Ralstonia solanacearum, Phytophthora infestans, and Neopestalotiopsis javaensis responsible for causing banana bacterial wilt, late blight y scab diseases, respectively. The extracts were obtained in methanol. The phytopathogens were isolated from diseased plants grown in Ecuador, R. solanacearum was isolated from samples of Musa paradiasiaca, P. infestans from samples of Solanum lycopersicum and N. javaensis from diseased samples of Persea americana—morphological and molecular methods identified the isolated pathogens. The antibacterial activity was determined by the microtiter broth dilution method; six serial concentrations of the extracts were tested. The antifungal activity was determined based on the effects of the plant extracts on the inhibition of radial growth of fungi; five serial concentrations of the extracts were tested. The extracts of P. prostrata and R. roseus showed activity against R. solanacearum and P. infestans with a MIC of 22.5 and 31.25 mg/mL, respectively.