<p>Agricultural intensification on existing arable lands has been proposed to reduce deforestation in the Congo Basin, although the effects of intensification on soil greenhouse gas (GHG) emissions have not yet been investigated. Here, we present the first field study to quantify the trade-offs between yield and GHG emissions across different intensification options in this region. We show that intercropping with nitrogen-fixing beans not only provided additional protein-rich food but also increased maize yields by 1.4-fold while leaving N₂O emissions and the soil CH₄ sink unchanged compared to unfertilized maize. In contrast, a moderate mineral fertilizer application of 66 kg N ha⁻¹ yr⁻¹ doubled yields, but reduced the soil CH₄ sink strength, and increased N₂O emissions fivefold to about 4 kg N₂O-N ha⁻¹ yr⁻¹. These N₂O emissions also exceeded those of natural forests by more than a factor of three, highlighting the GHG cost of mineral fertilizer use in addition to CO₂ emissions from soil organic carbon loss following land conversion. In sum, intercropping with nitrogen-fixing beans had the lowest yield-scaled GHG emissions and can help to address protein malnutrition in regions with limited access to mineral fertilizers or particularly high N₂O emissions.</p>