Concerns about the impacts of climate change have led to increased targets for biofuel in the global energy market. First-generation biofuel crops contain oil, sugar or starch and are usually also grown for food, whereas second-generation biofuel is derived from non-food sources, including lignocellulosic crops, fast-growing trees, crop residues and waste. Biofuel production drives land-use change, a major cause of biodiversity loss, but there is limited knowledge of how different biofuel crops affect local biodiversity. Therefore, a more detailed understanding could inform more environmentally-conscious decisions about where to grow which biofuel crops. We synthesised data from 116 sources where a potential biofuel crop was grown and estimated how two measures of local biodiversity, species richness and total abundance, responded to different crops. Local species richness and abundance were 37% and 49% lower at sites planted with first-generation biofuel crops than in sites with primary vegetation. Soybean, wheat, maize and oil palm had the worst effects; the worst affected regions were Asia and Central and South America; and plant species richness and vertebrate abundance were the worst affected biodiversity measures. Second-generation biofuels had smaller, but still significant, effects: species richness and abundance were 19% and 25%, respectively, lower in such sites than in primary vegetation. Our models suggest that land clearance to cultivate biofuel crops reduces local biodiversity. However, the yield of biofuel from different crops influences the biodiversity impacts per unit of energy generated, and the geographic and taxonomic variation in effects are also relevant for making sustainable land-use decisions.