SummaryHydrophilic extracts from plants contain anti-microbial macromolecules that may be considered when developing natural compounds to control plant pathogens, including anti-microbial peptides that differ structurally from commercial pesticides. This study evaluated the anti-microbial activities of aqueous peptide-enriched fractions from the leaves of bell pepper (Capsicum annuum L. ‘Magali R’) against phytopathogens for biotechnological applications. Fully-expanded bell pepper leaves were frozen, powdered and extracted. The supernatant was labelled the soluble extract (SE), and the precipitate was extracted with LiCl to produce a cell wall extract (CWE). The SE and CWE were then fractionated using ammonium sulphate following molecular exclusion chromatography. Electrophoresis showed that the CWE was a less complex extract. A peptide-enriched fraction (PF) from the CWE was then fractionated by hydrophobic chromatography. Two of the fractions recovered inhibited the growth of Ralstonia solanacearum and Clavibacter michiganensis ssp. michiganensis in vitro. For commercial-scale applications, ultrafiltration (1.0 – 10.0 kDa cut-off) replaced chromatography, for lower cost. The peptide sub-fraction CWE1-10kDa partially controlled the in vitro growth of R. solanacearum, C. michiganensis ssp. michiganensis, and Alternaria solani and showed high activity against Erwinia carotovora ssp. carotovora, with total inhibition at a low concentration of 96.7 mg peptide fruction l–1. CWE1-10kDa represents an aqueous anti-microbial extract that may complement the use of pesticides, and have lower environmental toxicity.