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Blue mold is one of the most serious postharvest diseases in apples caused by <i>Penicillium expansum</i>. The purpose of this study is to determine the effect of ε-poly-L-lysine (ε-PL) on the pathogenicity of <i>P. expansum</i> and explore the potential mechanism from the perspective of organic acid. The study investigates the effect of ε-PL treatment on the growth and acid production of <i>P. expansum</i> in vitro and in vivo. When the concentration of ε-PL was 50 mg/L, the growth of <i>P. expansum</i> was inhibited and the decrease in pH value was delayed in the medium. For example, on the third day of culture, <i>P. expansum</i> reduced the pH of the medium from 6.1 to 4.15, and ε-PL inhibited the decrease in the pH value at most 34.4%. When the concentration reached 1000 or 2000 mg/L, the infection of <i>P. expansum</i> in fruits was effectively inhibited. During the growth and infection of <i>P. expansum</i>, gluconic acid is one of the main factors leading to the pH value falling in the local environment. After ε-PL treatment, the accumulation of gluconic acid decreased, the activity of glucose oxidase was suppressed, and then the decline in the local environmental pH slowed down. In addition, after ε-PL treatment, the activities of cell-wall-degrading enzymes, such as cellulase (CL) and polygalacturonase (PG), in the different areas of the <i>P. expansum</i>–apple interaction were also affected by pH change. The results show that ε-PL inhibited the pathogenicity of <i>P. expansum</i> by affecting the accumulation of gluconic acid and slowing the decline in pH in fruit tissues, so as to affect the pathogenicity of <i>P. expansum</i>. This is the first time that the mechanism of ε-PL interfering with the pathogenicity of <i>P. expansum</i> from the perspective of organic acids is clarified.