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The experiment was conducted using the stem and root bark extract of Azadirachta indica and the root bark extract of Vernonia amygdalina at 10% concentration. The pepper fruits were dipped in each extract for five minutes and air dried after which 1mm agar plugs of Colletotrichum capsici were used to inoculate the fruits. The root, stem bark extract of A. indica and the root bark extract of V. amygdalina significantly (P ≤ 0.05) reduced the lesion diameter of C. capsici by 94%, 68% and 20% respectively. Pepper fruits treated with the root bark extract of A. indica had a severity of 2.05 while pepper fruits treated with the root bark extract of V. amygdalina and A. indica both had a severity value of 2.33. Capsicum frutescens fruits inoculated with C. capsici alone had the highest severity value of 4.47. Treating pepper fruits with the root bark extract of V. amydalina and A. indica significantly (P≤ 0.05) reduced decay of C. frutescens by 76% and 86% respectively. Total soluble solid (TSS) of pepper fruits treated with the root bark extract of A. indica was significantly (P≤0.05) lower (7.50°brix) compared with the TSS value of the control (9.20°brix). The root and stem bark extract of A. indica can be utilized as an alternative to synthetic chemicals in the treatment of pepper fruits to reduce pepper anthracnose and increase pepper fruit quality.