Irradiation of foods and fruits by ionizing radiation effectively eliminates pathogenic microorganisms primarily present on the surface. Recently, much attention has been paid to the use of low-energy X-rays and electron beams for food irradiation. Dosimetric investigation of foods with complex shapes is experimentally challenging. In this study, a multiscale Monte Carlo simulation was performed to compare the dose distributions of low-energy X-rays and electrons in a typical-size apple as well as to calculate the DNA damages induced by secondary electrons in a bacterial cell model. Several energies up to 500 keV and tube voltages up to 200 kV were considered for incident electrons and X-rays, respectively. The results indicate that on a microscopic scale, the yields of single- and double-stranded DNA breaks induced by X-rays and electrons of different energies are nearly identical. In a macroscopic scale, a two-sided electron beam configuration plus a 90-degree rotation of the apple (or the beam) provides an appropriate dose uniformity on the apple surface up to a depth of 40 μm. In the case of low-energy X-rays, apple rotation is not required when a two-sided irradiation is applied. Generally, X-rays are superior to electrons for the surface treatment of apples due to their lower dose uniformity ratios on the surface.