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Abstract This study aimed to evaluate the effects of inoculants on the microbial community and mycotoxins contamination of corn silage during aerobic exposure. Whole-crop corn infected with or without mycotoxigenic fungi were ensiled with Lentilactobacillus buchneri (LB, 1.0 × 106 cfu/g fresh weight (FW)), Lactiplantibacillus plantarum (LP, 1.0 × 106 cfu/g FW), or LBLP at 1.0 × 106 cfu/g FW each. The concentration of acetic acid (AcA) (P < 0.05) in LB and LBLP silages was higher than in control (C) and LP of non-fungal infection (NFI) silages. The fungal infection resulted in a larger increase of zearalenone (ZEN, P = 0.01), fumonisin B1 (FUB1, P = 0.02), and fumonisin B2 (FUB2, P = 0.02). The relative abundance (RA) of Issatchenkia in NFI was higher (P < 0.001) than FI silages, whereas the RA of Kazachstania (P < 0.001), Zygosaccharomyces (P = 0.047), and Candida (P = 0.025) in NFI were lower than these of FI silages. The aerobic stability was improved by the application of LB and LBLP as compared with the C of NFI silages. The LB and LBLP had the potential to improve aerobic stability and alleviate mycotoxins contamination of non-fungal infected corn silages. Graphical Abstract