Background The microbiological safety of donor milk (DM) is commonly ensured by Holder pasteurization (HoP, 62.5 °C for 30 min) in human milk banks despite its detrimental effects on bioactive factors. We compared the antimicrobial properties of DM after Holder pasteurization treatment or High Hydrostatic Pressure processing (HHP, 350 MPa at 38 °C), a non-thermal substitute for DM sterilization. Methods We assessed lactoferrin and lysozyme concentrations in raw, HHP- and HoP-treated pools of DM (n = 8). The impact of both treatments was evaluated on the growth of Escherichia coli and Group B Streptococcus in comparison with control media (n = 4). We also addressed the effect of storage of HHP treated DM over a 6-month period (n = 15). Results HHP milk demonstrated similar concentrations of lactoferrin compared with raw milk, while it was significantly decreased by HoP. Lysozyme concentrations remained stable regardless of the condition. Although a bacteriostatic effect was observed against Escherichia coli at early timepoints, a sharp bactericidal effect was observed against Group B Streptococcus. Unlike HoP, these results were significant for HHP compared to controls. Stored DM was well and safely preserved by HHP. Conclusion Our study demonstrates that this alternative sterilization method shows promise for use with DM in human milk banks. Impact Antimicrobial activity of donor milk after High Hydrostatic Pressure treatment has not been clearly evaluated. Donor milk lactoferrin is better preserved by High Hydrostatic Pressure than conventional Holder pasteurization, while lysozyme concentration is not affected by either treatment. As with Holder pasteurization, High Hydrostatic Pressure preserves donor milk bacteriostatic activity against E. coli in addition to bactericidal activity against Group B Streptococcus. Donor milk treated by High Hydrostatic Pressure can be stored safely for 6 months.