The link between global ecosystem decline, trade, and human consumption suggests that trade-based biodiversity footprints should be regarded as a critical indicator of planetary impacts. Here we integrate a global input-output economic framework that encompasses global trade between 15909 sectors, with range and impact data on 10518 terrestrial plant, 17234 terrestrial animal, 6101 freshwater and 5059 marine species, to specify the biodiversity footprints associated with global trade and consumption across domestic and international supply chains. Our framework characterises global species loss as driven by domestic trade in emerging market economies including China, Brazil, Mexico, India, and Ecuador, and exacerbated by consumption in high-income countries, especially those in the G7, that are driving species loss in emerging markets and low-income nations. We attribute the largest sector-scope footprints to construction in China, Colombia, and India, agriculture commodity trade in Madagascar, Mexico, Tanzania, and Peru, and food manufacture in Mexico, Germany and France.