<p>Declining soil fertility remains a critical barrier to sustainable agriculture and food security. Although chemical fertilizers enhance crop yields, their long-term use is unsustainable. Legume-based cropping systems combined with organic fertilizers offer a more ecologically sustainable alternative. The purpose of this study was to evaluate the effects of integrating maize–soybean intercropping with black soldier fly frass fertilizer (BSFFF) on grain yield, soil carbon sequestration, and nutrient dynamics across two agro-ecological zones: Quzhou, Hebei Province, China, and Lisasadzi, Kasungu District, Malawi. A split-plot design was implemented, with cropping systems—sole maize (MZ), sole soybean (SB), and maize–soybean intercropping (MZ + SB)—as main plots, and fertilizer treatments—no fertilizer (CK), sole BSFFF, synthetic fertilizer (NPK), and combination of BSFFF and NPK (½BSFFF+½NPK)—as subplots. All treatments were replicated three times. Results showed that intercropping improved land productivity (LER = 1.10 in Lisasadzi and LER = 1.06 in Quzhou) compared to sole cropping. The ½BSFFF+½NPK treatment in the intercropping system yielded the highest productivity, increasing grain yield by 14% in Lisasadzi and 9% in Quzhou. Sole BSFFF treatment also improved yields by 12% and 8%, respectively. BSFFF-amended plots recorded higher soil organic carbon (SOC) (42.9% in Lisasadzi; 25% in Quzhou), available phosphorus (10.0% and 18.2%), and available potassium (4.9% and 6.0%) compared to NPK-treated plots. These findings suggest that integrating BSFFF with maize–soybean intercropping improves crop productivity, enhances soil health, and boosts nutrient use efficiency. This approach offers a sustainable and adaptable alternative to chemical fertilizers for enhancing food production and soil resilience across diverse agro-ecological environments.</p> Graphical abstract <p></p>