Fruit byproducts are considered a high source of bioactive molecules, which possess antioxidant activities. These antioxidants play principal functions in mycotoxin reduction. This study aimed to evaluate crude mandarin byproduct extract for its chemical interaction with fungal growth and suppression of mycotoxin production, and to illustrate whether the impact was regarding individual molecules or a synergistic antioxidation process. Extract contents were analyzed for their phenolic, flavonoids, and antioxidant activity. The fatty acid composition and volatile components were determined using the GC apparatus. The influence of the extract evaluated versus the standard phenolics of trans-ferulic and hesperidin were evaluated. The liposome technique was applied to prevent the antioxidant properties of the bioactive extract. The anti-mycotoxigenic effects of the liposomal and non-liposomal extract were determined in fungal media against the standard phenolics. The results manifested ferulic (235.54 ± 3.34 mg/100 g) and hesperidin (492.11 ± 1.15 mg/100 g) as high phenolics in the extract. Limonene was the main volatile (67.54 ± 1.74%), as well antioxidant activities determined in considerable values. The crude extract recorded efficiency as an anti-Fusarium agent, but less than the standard hesperidin applied in fungal media. The bioactive extract recorded possessed a reduction influence on mycotoxin production. The impact may be joining with its fungal inhibition or its component activity with the active groups on the mycotoxin molecule. The formation of liposomal extract enhanced its efficacy in mycotoxin reduction. This enhancement may illustrate its protective properties for antioxidant components of the bioactive extract.