Aflatoxin B1 contamination in stored maize, primarily caused by Aspergillus flavus, poses a significant threat to food safety and public health. This study aims to evaluate the antifungal efficacy of Senna occidentalis seed extract and Hyptis suaveolens essential oil as natural alternatives to synthetic fungicides. A. flavus was isolated from infected maize kernels and confirmed through DNA extraction, PCR amplification of the ITS region, and BLAST analysis, which revealed 100% sequence identity with GenBank accession OR646810.1. Plant materials were extracted using ethanol maceration (S. occidentalis) and steam distillation (H. suaveolens), followed by GC-MS profiling. Maize grains were treated with 5 mL, 10 mL, and 15 mL doses of each extract and stored for 30 days at 30 °C. Aflatoxin B1 levels were quantified using high-performance liquid chromatography (HPLC). The research findings showed that untreated maize contained 101 ± 1.0 µg/kg aflatoxin B1, while grains treated with synthetic fungicide (SAAF) had 5.0 ± 0.1 µg/kg (98% inhibition). S. occidentalis extract reduced aflatoxin levels to 15.3 ± 1.0, 10.3 ± 1.0 and 6.3 ± 1.0 µg/kg at 5 mL, 10 mL, and 15 mL doses, respectively (85–94% inhibition). H. suaveolens essential oil achieved reductions to 20.3 ± 1.0, 13.3 ± 1.0 and 8.3 ± 1.0 µg/kg (80–92% inhibition). The 15 mL dosage was the most effective for both treatments, approaching the efficacy of the synthetic fungicide. The antifungal activity is attributed to phytol, linoleic acid and esters in S. occidentalis, and terpenes such as eucalyptol and caryophyllene in H. suaveolens. These findings demonstrate the potential of plant-based treatments as eco-friendly and effective alternatives for aflatoxin mitigation in maize storage systems.