Increasing population size and demand for food in the developing world is driving the intensification of agriculture, often threatening the biodiversity within the farmland itself and in the surrounding landscape. This paper quantifies bird and tree species richness, tree carbon and farmer's gross income, and interactions between these four variables, across an agricultural gradient in central Uganda. We showed that higher cultivation intensities in farmed landscapes resulted in increased income but also a decline in species richness of birds and trees, and reductions in tree carbon storage. These declines were particularly marked with a shift from high intensity smallholder mixed cropping to plantation style agriculture. This was especially evident for birds where significant declines only occurred in plantations. Small scale farming will likely continue to be a key source of cash income for the rural populations, and ensuring ‘sustained agricultural growth’ within such systems while minimising negative impacts on biodiversity and other key ecosystem services will be a major future challenge.