The objective of the present study was to determine if application of microfiltration (MF) or raw milk lactoperoxidase system (LP) could reduce the risk of foodborne illness from Escherichia coli in raw milk cheeses, without adversely affecting the overall sensory acceptability of the cheeses. Escherichia coli K12 was added to raw milk to study its survival as a non-pathogenic surrogate organism for pathogenic E. coli. Five replications of 6 treatments of Cheddar cheese were manufactured. The 6 treatments included cheeses made from pasteurized milk (PM), raw milk (RM), raw milk inoculated with E. coli K12 (RME), raw milk inoculated with E. coli K12 + LP activation (RMELP), raw milk inoculated with E. coli K12 + MF (MFE), and raw milk inoculated with E. coli K12 + MF + LP activation (MFELP). The population of E. coli K12 was enumerated in the cheese milks, in whey/curds during cheese manufacture, and in final Cheddar cheeses during ripening. Application of LP, MF, and a combination of MF and LP led to an average percentage reduction of E. coli K12 counts in cheese milk by 72, 88, and 96%, respectively. However, E. coli K12 populations significantly increased during the manufacture of Cheddar cheese for the reasons not related to contamination. The number of E. coli K12, however, decreased by 1.5 to 2 log cycles during 120 d of ripening, irrespective of the treatments. The results suggest that MF with or without LP significantly lowers E. coli count in raw milk. Hence, if reactivation of E. coli during cheese making could be prevented, MF with or without LP would be an effective technique for reducing the counts of E. coli in raw milk cheeses. The cheeses were also analyzed for proteolysis, starter and nonstarter lactic acid bacteria (NSLAB), and sensory characteristics during ripening. The concentration of pH 4.6 soluble nitrogen at 120 d was greater in PM cheese compared with the other treatments. The level of 12% trichloroacetic acid-soluble nitrogen at 120 d was greater in RM, RME, and RMELP cheeses compared with PM, MFE, and MFELP cheeses. This could be related to the fact that cheeses made from raw milk with or without LP (RM, RME, and RMELP) had greater levels of NSLAB compared with PM, MFE, and MFELP cheeses. Cheeses at 60 d, as evaluated by 8 trained panelists, did not differ in bitterness, pastiness, or curdiness attributes. Cheeses at 120 d showed no differences in acid-taste, bitterness, or curdiness attributes. Sensory analysis at 60 d showed that PM and MFELP cheeses had greater overall sensory acceptability than RM and RME cheeses. The overall sensory acceptability of the cheeses at 120 d showed that PM, MFE, and MFELP cheeses were more acceptable than RM and RME cheeses.