Ultraviolet-C (UV-C 254 nm) light is a possible alternative for chemical disinfection of fresh fruits. However, studies on the influence of surface characteristics on the kinetics of UV-C inactivation of microorganisms on fruits are limited. In this study, UV-C inactivation of generic Escherichia coli (ATCC 23716), a nonpathogenic surrogate strain for E. coli O157:H7, was inoculated onto the skin surface intact pear, pear with surface wounds, and the skin surface of intact peach. Disc shaped (0.057 m diameter × 0.01 m height) fruit surface were exposed at room temperature to UV-C light ranging from 0 to 7.56 ± 0.52 kJ/m2 and microbial inactivation kinetics was determined. Maximum reductions of 3.70 ± 0.125 log CFU/g were achieved for E. coli on intact pear surfaces (P < 0.05), with lesser reduction on wounded pear (3.10 ± 0.329 log CFU/g) and peach surfaces (2.91 ± 0.284 log CFU/g) after 4 min UV-C exposure at 7.56 kJ/m2 UV. The Weibull scale factor (α) values of UV-C inactivation for E. coli on an intact pear surface was 0.001 ± 0.0007 min (0.235 ± 0.001 kJ/m2), wounded pear surface, 0.003 ± 0.001 min (0.240 ± 0.002 kJ/m2) and peach surface, 0.004 ± 0.0004 (0.241 ± 0.0008 kJ/m2). The time required for a 90 % reduction in E. coli cell numbers or the reliable life time (t R) calculated with the Weibull model for intact pear surfaces (0.019 ± 0.009 min, 0.268 ± 0.017 kJ/m2) was smaller than for wounded pear (0.062 ± 0.013 min, 0.348 ± 0.024 kJ/m2) and peach surfaces (0.074 ± 0.012, 0.371 ± 0.012 kJ/m2), suggesting that the wounds on pear surfaces and trichomes (100–1000 μm) on peach surfaces helped to shield and protect microorganisms from UV-C radiation. There was likely a more uniform distribution of bacterial cells onto pear surfaces due to its smaller surface roughness, spreading coefficient, and hydrophobic nature compared to peach. Fourier transform infrared spectroscopy indicate that bacterial membrane damage (phospholipids, protein secondary structures, and polysaccharides) and changes to DNA/RNA in E. coli resulted from UV-C treatment. UV-C can reduce E. coli populations on fresh fruit surfaces, but the efficacy of UV treatment is dependent upon the morphological and surface properties of the fruit and surface integrity.