Several methods have been described to prepare fresh produce samples for microbiological analysis, each with its own advantages and disadvantages. The aim of this study was to compare the performance of a novel combined rinse and membrane filtration method to two alternative sample preparation methods for the quantification of indicator microorganisms from fresh produce. Decontaminated cantaloupe melons and jalapeño peppers were surface inoculated with a cocktail containing 10(6) CFU/ml Escherichia coli, Salmonella Typhimurium, and Enterococcus faecalis. Samples were processed using a rinse and filtration method, homogenization by stomacher, or a sponge-rubbing method, followed by quantification of bacterial load using culture methods. Recovery efficiencies of the three methods were compared. On inoculated cantaloupes, the rinse and filtration method had higher recovery of coliforms (0.95 log CFU/ml higher recovery, P = 0.0193) than the sponge-rubbing method. Similarly, on inoculated jalapeños, the rinse and filtration method had higher recovery for coliforms (0.84 log CFU/ml higher, P = 0.0130) and E. coli (1.46 log CFU/ml higher, P < 0.0001) than the sponge-rubbing method. For jalapeños, the rinse and filtration method outperformed the homogenization method for all three indicators (0.79 to 1.71 log CFU/ml higher, P values ranging from 0.0075 to 0.0002). The precision of the three methods was also compared. The precision of the rinse and filtration method was similar to that of the other methods for recovery of two of three indicators from cantaloupe (E. coli P = 0.7685, E. faecalis P = 0.1545) and was more precise for recovery of two of three indicators from jalapeño (coliforms P = 0.0026, E. coli P = 0.0243). Overall, the rinse and filtration method performed equivalent to, and sometimes better than, either of the compared methods. The rinse and filtration method may have logistical advantages when processing large numbers of samples, improving sampling efficiency and facilitating microbial detection.