Alternaria sp. causes discoloration and black spot disease in Pyrus pyrifolia (Japanese or Nashi pear). We investigated the antimicrobial properties of an emulsion oil of natural antimicrobial substances, such as allyl isothiocyanate (AITC) and lemongrass oil. The effect of oil-droplet size in the emulsified oil containing AITC and lemongrass oil with modified starch was assessed. Furthermore, the effect of different oil ratios on the antimicrobial properties was also investigated. When the emulsion oil weight ratio of AITC to lemongrass oil was 0.15, Alternaria sp. growth was not observed after 16 days. In paper bags coated with the emulsified oil, the amount of lemongrass oil retained on the paper increased with a decrease in the average oil-droplet size.