Australia's northern savannas are one of the few remaining large and mostly intact natural areas on Earth. However, their biodiversity and ecosystem values could be threatened if proposed agricultural development proceeds. Through land-use change scenarios, we explored trade-offs and synergies among biodiversity conservation, carbon farming and agriculture production in northern Australia. We found that if all suitable soils were converted to agriculture, habitat at unique recorded locations of three species would disappear and 40 species and vegetation communities could lose more than 50% of their current distributions. Yet, strategically considering agriculture and biodiversity outcomes leads to zoning options that could yield >56,000 km2 of agricultural development with a significantly lower impact on biodiversity values and carbon farming. Our analysis provides a template for policy-makers and planners to identify areas of conflict between competing land-uses, places to protect in advance of impacts, and planning options that balance agricultural and conservation needs.