Brown rot caused by Monilinia spp. is the most important postharvest disease of stone fruit. From preliminary studies, the combination of 0.25% hydrogen peroxide, 0.02% peracetic acid (PAA) and 0.075% acetic acid, corresponding to 300 mg L−1 of PAA, was selected to control Monilinia fructicola. Brown rot control was similarly controlled when the same concentration of PAA was applied with a PAA-based commercial product. In order to reduce PAA concentration, combinations of different concentrations and temperatures were evaluated. A treatment of 200 mg L−1 of PAA at 40 °C for 40 s was selected to control pre-existing and future infections, different inoculum concentrations of M. fructicola and to control brown rot on naturally infected fruit. Brown rot was completely controlled with the selected treatment when peaches and nectarines were inoculated 0 h before the treatment but it was not controlled when infection time was increased to 24, 48 and 72 h. Also, the treatment significantly controlled brown rot at all inoculum concentrations evaluated (103, 104, 105 and 106 conidia mL−1) in both peaches and nectarines, but no protection against future infections was observed. In naturally infected fruit, brown rot incidence was slightly but significantly reduced to 61 and 36% in 'Roig d'Albesa' and 'Placido' peaches, respectively, but not in nectarines. Immersion for 40 s in 200 mg L−1 of PAA at 40 °C provides an alternative treatment to control only recent infections of Monilinia spp. whatever their concentration without generally affecting fruit quality.