Hundreds of dams have been proposed throughout the Amazon basin, one of the world’s largest untapped hydropower frontiers. While hydropower is a potentially clean source of renewable energy, some projects produce high greenhouse gas (GHG) emissions per unit electricity generated (carbon intensity). Here we show how carbon intensities of proposed Amazon upland dams (median = 39 kg CO2eq MWh−1, 100-year horizon) are often comparable with solar and wind energy, whereas some lowland dams (median = 133 kg CO2eq MWh−1) may exceed carbon intensities of fossil-fuel power plants. Based on 158 existing and 351 proposed dams, we present a multi-objective optimization framework showing that low-carbon expansion of Amazon hydropower relies on strategic planning, which is generally linked to placing dams in higher elevations and smaller streams. Ultimately, basin-scale dam planning that considers GHG emissions along with social and ecological externalities will be decisive for sustainable energy development where new hydropower is contemplated.