Smallholder farm-households produce most of the crop and livestock products consumed in developing countries. Equitable transitions to low emissions food production will depend on policies that promote a reduction of greenhouse gases (GHGs) whilst improving these farmers’ livelihoods. Here, using survey data and simulation modelling, we show that Tanzania’s public programme to reduce import dependence through efficiency gains in the dairy sector increases farmer incomes (+12-20%) whilst reducing GHG emissions consistent with the Nationally Determined Contributions pledge (21-39%). Scenario analysis demonstrates that incrementally higher proportions of improved cattle (Bos taurus crosses) in the herd lead to greater reductions in GHGs over the Baseline, whilst benefitting producers through higher marketable surpluses and household income. As East Africa has the highest population density of indigenous Bos indicus cattle in Africa, genetic gains will be a key lever for reconciling food sovereignty with climate mitigation pledges throughout the region.