Even though the green revolution was a significant turning point in agriculture, it was also marked by the widespread use of chemical pesticides, which prompted severe concerns about their influence on human and environmental health. As a result, the demand for healthier and more environmentally friendly alternatives to control plant diseases and avoid food spoilage is intensifying. Among the proposed alternatives, food by-product extracts, especially from the most consumed fruits in Egypt, eggplant, sugar apple, and pomegranate peel wastes, were largely ignored. Hence, we chose them to evaluate their antifungal and antiaflatoxigenic activities against maize fungus, Aspergillus flavus. All the extracts exhibited multiple degrees of antifungal growth and aflatoxin B1 (AFB1) inhibitory activities (35.52% to 91.18%) in broth media. Additionally, diethyl ether 50% eggplant, ethanol 75% sugar apple, and diethyl ether 25% pomegranate extracts exhibited the highest AFB1 inhibition, of 96.11%, 94.85%, and 78.83%, respectively, after one month of treated-maize storage. At the same time, Topsin fungicide demonstrated an AFB1 inhibition ratio of 72.95%. The relative transcriptional levels of three structural and two regulatory genes, aflD, aflP, aflQ, aflR, and aflS, were downregulated compared to the infected control. The phenolic content (116.88 mg GAEs/g DW) was highest in the 25% diethyl ether pomegranate peel extract, while the antioxidant activity was highest in the 75% ethanol sugar apple extract (94.02 µg/mL). The most abundant active compounds were found in the GC-MS analysis of the fruit peel extracts: α-kaurene, α-fenchene, p-allylphenol, octadecanoic acid, 3,5-dihydroxy phenol, hexestrol, xanthinin, and linoleic acid. Finally, the three fruit peel waste extracts could be a prospective source of friendly ecological compounds that act as environmentally safer and more protective alternatives to inhibit AFB1 production in maize storage.