The overreliance on synthetic pesticides for stored-grain protection presents environmental and health concerns, highlighting the need for safer plant-based alternatives. This study evaluated the biopesticidal efficacy of onion peel, ginger, and alligator pepper formulations against storage fungi and insect pests (Sitophilus zeamais and Callosobruchus maculatus) infesting maize and cowpea. The plant materials were prepared as powders, aqueous extracts, and hexane oil extracts. Phytochemical screening and GC–MS profiling confirmed phenolics, alkaloids, flavonoids, glycosides, and tannins, with decanal (11.53%) in ginger, dodecadiene (7.01%) in onion peel, and octadecanoic acid (31.96%) in alligator pepper identified as major constituents. Antifungal activity was assessed via radial mycelial inhibition at five concentrations (0.2–1.0 g), while insect bioefficacy was evaluated at 1.0–3.0 g/50 g grain over 60 days. The aqueous extract of alligator pepper showed the strongest antifungal effect, restricting A. flavus and Penicillium spp. growth to 1.0 cm after 24 hours. Ginger aqueous extract at 3.0 g/50 g reduced maize grain damage and weight loss to 1.20 ± 0.20% and 1.33 ± 1.15%, compared with 38.42 ± 4.62% and 12.66 ± 8.33% in untreated controls (p < 0.05). Ginger oil extract at 3.0 g/50 g lowered cowpea damage (10.96 ± 1.00%) and weight loss (0.60 ± 0.20%) relative to controls (32.75 ± 8.86% and 7.78 ± 2.10%). Overall, ginger and alligator pepper extracts exhibited potent antifungal and insecticidal activity, demonstrating strong potential as sustainable, cost-effective botanical alternatives for integrated postharvest management of stored grains in tropical regions.