Aims. To minimize fumonisins (FBs) accumulation by Fusarium verticillioides in post-harvest maize, using flavonoids obtained from citrus residues: naringin (NAR), neohesperidin (NEO), quercetin (QUER), and its mixtures. Methods and Results. Response surface methodology with Box-Behnken design was applied in maize at 0.98 and 0.95 aw. The optimal mixture found, composed of 0.40 mmol kg-1 NAR, 0.16 mmol kg-1 NEO and 0.37 mmol kg-1 QUER, reduced the accumulation of FBs B1, B2, and B3 by 88±6%, 90±6% and 85±5%, respectively, when applied to maize at 0.98 aw. The mentioned mixture led to a 54±9% reduction of fumonisin B1 accumulation in maize adjusted to 0.95 aw. These flavonoids applied individually and as a mixture, affected the structure of both the cell wall and the cytoplasm of F. verticillioides. The cell wall lost rigidity and the cells appeared highly deformed, with ruptured plasmalemma and disrupted endomembranes. Conclusions. It was possible to diminish the accumulation of FBs in maize by a highly toxigenic Fusarium strain, producing severe damage to its ultrastructure. Significance and Impact of Study. The results indicate the possible use of flavonoids from citrus industry residues as natural and environmentally friendly antifungal agents to restrain the accumulation of FBs in stored maize. © 2021 The Society for Applied Microbiology.