Monilinia spp. are the most important causes of brown rot in stone fruit and no chemical fungicides are allowed in the European Union to be applied to stone fruit after harvest. From preliminary studies, microwave (MW) treatments at 17.5 kW for 50 s and 10 kW for 95 s were selected as effective conditions to control brown rot. Both treatments were investigated to control Monilinia fructicola in fruit with different weights and maturity levels and in naturally infected fruit. Fruit weight only had a significant effect on microwave efficacy in 'Placido' peaches treated by MW at 10 kW for 95 s in which better brown rot control was observed in small than large fruit. Maturity level did not have a significant effect on efficacy of MW treatments in any of the varieties evaluated. When both MW treatments were studied in naturally infected peaches and nectarines, brown rot incidence was significantly reduced to less than 14% compared with untreated fruit where brown rot incidence was higher than 45%. The effect of both treatments on fruit quality was also evaluated. Fruit firmness was not negatively affected in the varieties tested and even a delay of fruit softening was observed. However, internal damage around the stone was observed, especially in the smallest fruit in which high temperature is achieved at the end of both MW treatments.