Peanuts and corn are susceptible to various soil-borne fungi, leading to significant economic losses. Atoxigenic Aspergillus flavus have been widely used as biocontrol agents for managing aflatoxin contamination because of their minimal environmental impact, strong competitive ability, and sustained inhibition effect. After multiple identifications and cluster amplification pattern (CAP) analysis, three atoxigenic A. flavus PA04, PA10 and PA67 were isolated from peanut samples in Shandong Province, which can reduce aflatoxin levels by up to 90 %. Our study revealed that atoxigenic A. flavus also competed vigorously with Sclerotium rolfsii and Fusarium proliferatum for nutrition and space, achieving notable inhibition rates of up to 90.4 % and 90.6 %, respectively. The supernatants of atoxigenic A. flavus also inhibited the growth of S. rolfsii and F. proliferatum, with PA67 demonstrating the most significant effect. Whole genome sequencing revealed that PA67 contains multiple glycoside hydrolases and metabolites with antifungal activity. The kojic acid production of PA67 was higher than that of PA04 and PA10, reaching 17.48 g/L, which has a significant inhibition on sclerotia germination. PA67 supernatant significantly inhibited the hyphae growth of S. rolfsii and F. proliferatum, and down-regulated genes related to sclerotia and fumonisin formation. This study demonstrates the biocontrol potential of PA67 against three soil-borne fungi and is the first investigation of atoxigenic A. flavus to inhibit S. rolfsii and F. proliferatum.